9d0b167a9ea9f20e7d06fb51e4688672eb583f9d hiram Mon Aug 17 12:19:47 2020 -0700 Added ambMex2; refs #23367 diff --git src/hg/makeDb/genbank/etc/genbank.conf src/hg/makeDb/genbank/etc/genbank.conf index af945b1..8ab7d1e 100644 --- src/hg/makeDb/genbank/etc/genbank.conf +++ src/hg/makeDb/genbank/etc/genbank.conf @@ -1,4960 +1,4984 @@ # configuration file for GenBank/RefSeq alignment process # # $Id: genbank.conf,v 1.371 2010/05/28 17:59:39 chinhli Exp $ # ## # cluster configuration ## # swarm cluster.rootDir = /hive/data/outside/genbank/build cluster.paraHub = ku.gi.ucsc.edu ## # only allow build on designated server ## build.server = genbank ## # Root where grepIndex files are build ## grepIndex.rootDir = /data/tmp/grepIndex ## # default values, which can be overridden for each genome ## ## # Alignment genome partition window and overlap sizes. Default values were # chosen to balance number of jobs, average run time and longest jobs for # human mRNA alignments. ## default.align.window = 80000000 default.align.overlap = 3000000 default.align.maxGap = 3000000 default.align.maxJobTargetSize = 80000000 ## # Minimum size of an unplaced seq to process, smaller sequences are skipped. # Value suggested by Jim Kent. "logical place to cut off is 'contigs' that # are composed of single reads, the single read size these days tends to be # about 750. So perhaps a cut off of 900." default.align.minUnplacedSize = 900 ## # max size of query fasta files to create, in megabytes. ## default.align.querySplitSize = 4 ## # pslCDnaFilter parameters variable definitions by genome assembly category, # and type of cDNA sequence. # # The assembly categories are: # - finished - high quality # - ordered - well ordered, whole genome shotgun # - lowCover - low coverage (< 4x), lots of contigs, N50 scaffold size < 1mb ## # common paramters used for all assembly categories var.common.refseq.mrna.native.pslCDnaFilter = -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes var.common.refseq.mrna.xeno.pslCDnaFilter = -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes var.common.genbank.mrna.native.pslCDnaFilter = -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes var.common.genbank.mrna.xeno.pslCDnaFilter = -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes var.common.genbank.est.native.pslCDnaFilter = -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes -usePolyTHead var.common.genbank.est.xeno.pslCDnaFilter = -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes -usePolyTHead # common paramters used for local near best filtering var.localNB.refseq.mrna.native.pslCDnaFilter = -localNearBest=0.001 ${common.refseq.mrna.native.pslCDnaFilter} var.localNB.refseq.mrna.xeno.pslCDnaFilter = -localNearBest=0.010 ${common.refseq.mrna.xeno.pslCDnaFilter} var.localNB.genbank.mrna.native.pslCDnaFilter = -localNearBest=0.005 ${common.genbank.mrna.native.pslCDnaFilter} var.localNB.genbank.mrna.xeno.pslCDnaFilter = -localNearBest=0.010 ${common.genbank.mrna.xeno.pslCDnaFilter} var.localNB.genbank.est.native.pslCDnaFilter = -localNearBest=0.005 ${common.genbank.est.native.pslCDnaFilter} var.localNB.genbank.est.xeno.pslCDnaFilter = -localNearBest=0.010 ${common.genbank.est.xeno.pslCDnaFilter} # common paramters used for global near best filtering var.globalNB.refseq.mrna.native.pslCDnaFilter = -globalNearBest=0.0010 ${common.refseq.mrna.native.pslCDnaFilter} var.globalNB.refseq.mrna.xeno.pslCDnaFilter = -globalNearBest=0.0100 ${common.refseq.mrna.xeno.pslCDnaFilter} var.globalNB.genbank.mrna.native.pslCDnaFilter = -globalNearBest=0.0025 ${common.genbank.mrna.native.pslCDnaFilter} var.globalNB.genbank.mrna.xeno.pslCDnaFilter = -globalNearBest=0.0100 ${common.genbank.mrna.xeno.pslCDnaFilter} var.globalNB.genbank.est.native.pslCDnaFilter = -globalNearBest=0.0025 ${common.genbank.est.native.pslCDnaFilter} var.globalNB.genbank.est.xeno.pslCDnaFilter = -globalNearBest=0.0100 ${common.genbank.est.xeno.pslCDnaFilter} # finished assemblies var.finished.refseq.mrna.native.pslCDnaFilter = -minId=0.95 -minCover=0.25 ${globalNB.refseq.mrna.native.pslCDnaFilter} var.finished.refseq.mrna.xeno.pslCDnaFilter = -minId=0.35 -minCover=0.25 ${globalNB.refseq.mrna.xeno.pslCDnaFilter} var.finished.genbank.mrna.native.pslCDnaFilter = -minId=0.95 -decayMinCover ${globalNB.genbank.mrna.native.pslCDnaFilter} var.finished.genbank.mrna.xeno.pslCDnaFilter = -minId=0.35 -minCover=0.25 ${globalNB.genbank.mrna.xeno.pslCDnaFilter} var.finished.genbank.est.native.pslCDnaFilter = -minId=0.95 -minCover=0.25 ${globalNB.genbank.est.native.pslCDnaFilter} var.finished.genbank.est.xeno.pslCDnaFilter = -minId=0.10 -minCover=0.10 ${globalNB.genbank.est.xeno.pslCDnaFilter} # well-ordered assemblies var.ordered.refseq.mrna.native.pslCDnaFilter = -minId=0.95 -minCover=0.15 ${localNB.refseq.mrna.native.pslCDnaFilter} var.ordered.refseq.mrna.xeno.pslCDnaFilter = -minId=0.35 -minCover=0.15 ${localNB.refseq.mrna.xeno.pslCDnaFilter} var.ordered.genbank.mrna.native.pslCDnaFilter = -minId=0.95 -minCover=0.15 ${localNB.genbank.mrna.native.pslCDnaFilter} var.ordered.genbank.mrna.xeno.pslCDnaFilter = -minId=0.35 -minCover=0.15 ${localNB.genbank.mrna.xeno.pslCDnaFilter} var.ordered.genbank.est.native.pslCDnaFilter = -minId=0.95 -minCover=0.15 ${localNB.genbank.est.native.pslCDnaFilter} var.ordered.genbank.est.xeno.pslCDnaFilter = -minId=0.35 -minCover=0.10 ${localNB.genbank.est.xeno.pslCDnaFilter} # low-coverage assemblies var.lowCover.refseq.mrna.native.pslCDnaFilter = -minId=0.94 -minAlnSize=80 ${localNB.refseq.mrna.native.pslCDnaFilter} var.lowCover.refseq.mrna.xeno.pslCDnaFilter = -minId=0.33 -minAlnSize=80 ${localNB.refseq.mrna.xeno.pslCDnaFilter} var.lowCover.genbank.mrna.native.pslCDnaFilter = -minId=0.94 -minAlnSize=80 ${localNB.genbank.mrna.native.pslCDnaFilter} var.lowCover.genbank.mrna.xeno.pslCDnaFilter = -minId=0.33 -minAlnSize=80 ${localNB.genbank.mrna.xeno.pslCDnaFilter} var.lowCover.genbank.est.native.pslCDnaFilter = -minId=0.94 -minAlnSize=50 ${localNB.genbank.est.native.pslCDnaFilter} var.lowCover.genbank.est.xeno.pslCDnaFilter = -minId=0.33 -minAlnSize=50 ${localNB.genbank.est.xeno.pslCDnaFilter} default.perChromTables = yes default.genbank.mrna.native.load = yes default.genbank.mrna.native.loadDesc = yes default.genbank.mrna.xeno.load = no default.genbank.mrna.xeno.loadDesc = no default.genbank.est.native.load = yes default.genbank.est.native.loadDesc = no default.genbank.est.xeno.load = no default.genbank.est.xeno.loadDesc = no default.refseq.mrna.native.load = yes default.refseq.mrna.native.loadDesc = yes default.refseq.mrna.xeno.load = yes default.refseq.mrna.xeno.loadDesc = yes ## # genome configurations ## # hg15test - used for debugging hg15test.serverGenome = /hive/data/genomes/hg15/nib/chr*.nib hg15test.ooc = /hive/data/genomes/hg15/11.ooc hg15test.lift = /hive/data/genomes/hg15/jkStuff/liftAll.lft #hg15test.align.unplacedChroms = chrUn_random hg15test.align.unplacedChroms = chr*_random hg15test.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} hg15test.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} hg15test.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} hg15test.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} hg15test.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} hg15test.mgc = yes hg15test.orfeome = yes hg15test.downloadDir = 10april1970 hg15test.genbank.mrna.blatTargetDb = yes hg15test.refseq.mrna.blatTargetDb = yes # hg16 hg16.serverGenome = /hive/data/genomes/hg16/hg16.2bit hg16.ooc = /hive/data/genomes/hg16/11.ooc hg16.lift = /hive/data/genomes/hg16/jkStuff/liftAll.lft hg16.align.unplacedChroms = chrUn_random hg16.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} hg16.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} hg16.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} hg16.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} hg16.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} hg16.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} hg16.genbank.est.xeno.load = yes hg16.genbank.mrna.xeno.load = yes hg16.mgc = yes hg16.upstreamGeneTbl = refGene hg16.upstreamMaf = mzPt1Mm3Rn3Gg2_pHMM /hive/data/genomes/hg16/bed/multiz.hg16mm3rn3panTro1galGal2/species.lst # hg17 hg17.serverGenome = /hive/data/genomes/hg17/hg17.2bit hg17.ooc = /hive/data/genomes/hg17/11.ooc hg17.lift = /hive/data/genomes/hg17/jkStuff/liftAll.lft hg17.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} hg17.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} hg17.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} hg17.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} hg17.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} hg17.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} hg17.genbank.mrna.xeno.load = yes hg17.genbank.est.xeno.load = yes hg17.refseq.mrna.xeno.load = yes hg17.refseq.mrna.xeno.loadDesc = yes hg17.mgc = yes hg17.orfeome = yes hg17.downloadDir = hg17 hg17.upstreamGeneTbl = refGene hg17.upstreamMaf = multiz17way /hive/data/genomes/hg17/bed/multiz17way/species.lst # hg18 hg18.serverGenome = /hive/data/genomes/hg18/hg18.2bit hg18.ooc = /hive/data/genomes/hg18/11.ooc hg18.lift = /hive/data/genomes/hg18/jkStuff/liftAll.lft hg18.hapRegions = /hive/data/genomes/hg18/bed/haplotypePos/haplotypePos.psl hg18.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} hg18.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} hg18.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} hg18.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} hg18.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} hg18.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} hg18.genbank.mrna.xeno.load = yes hg18.genbank.est.xeno.load = yes hg18.refseq.mrna.xeno.load = yes hg18.refseq.mrna.xeno.loadDesc = yes hg18.mgc = yes hg18.orfeome = yes hg18.downloadDir = hg18 hg18.ccds.buildId = 5 hg18.upstreamGeneTbl = refGene hg18.upstreamMaf = multiz28way /hive/data/genomes/hg18/bed/multiz28way/species.lst multiz44way /hive/data/genomes/hg18/bed/multiz44way/species.list hg18.genbank.mrna.blatTargetDb = yes # braNey1 - GRCh37 - Genome Reference Consortium Human Reference 37 # Assembly Accession: GCA_000001405.1 braNey1.serverGenome = /hive/data/genomes/hg19/hg19.2bit braNey1.ooc = /hive/data/genomes/hg19/11.ooc braNey1.lift = /hive/data/genomes/hg19/jkStuff/hg19.unBridged.lift braNey1.hapRegions = /hive/data/genomes/hg19/jkStuff/hg19.haplotypes.psl #braNey1.refseq.mrna.native.pslCDnaFilter = -maxAlignsDrop=50 -ignoreIntrons -repsAsMatch ${finished.refseq.mrna.native.pslCDnaFilter} braNey1.refseq.mrna.native.pslCDnaFilter = -ignoreIntrons -repsAsMatch ${finished.refseq.mrna.native.pslCDnaFilter} braNey1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} #braNey1.genbank.mrna.native.pslCDnaFilter = -maxAlignsDrop=50 -ignoreIntrons -repsAsMatch ${finished.genbank.mrna.native.pslCDnaFilter} braNey1.genbank.mrna.native.pslCDnaFilter = -ignoreIntrons -repsAsMatch ${finished.genbank.mrna.native.pslCDnaFilter} braNey1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} #braNey1.genbank.est.native.pslCDnaFilter = -maxAlignsDrop=50 -ignoreIntrons -repsAsMatch ${finished.genbank.est.native.pslCDnaFilter} braNey1.genbank.est.native.pslCDnaFilter = -ignoreIntrons -repsAsMatch ${finished.genbank.est.native.pslCDnaFilter} braNey1.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} braNey1.genbank.mrna.xeno.load = no braNey1.genbank.est.xeno.load = no braNey1.refseq.mrna.xeno.load = yes braNey1.refseq.mrna.xeno.loadDesc = yes braNey1.mgc = yes braNey1.orfeome = yes braNey1.downloadDir = hg19 braNey1.upstreamGeneTbl = refGene braNey1.upstreamMaf = multiz46way /hive/data/genomes/hg19/bed/multiz46way/species.list braNey1.genbank.mrna.blatTargetDb = yes braNey1.perChromTables = no braNey1.addVersionToTables = yes # braNey38 - GRCh38 - Genome Reference Consortium Human Reference 38 # Assembly Accession: GCA_000001405.1 braNey38.serverGenome = /hive/data/genomes/hg38/hg38.2bit braNey38.ooc = /hive/data/genomes/hg38/hg38.11.ooc braNey38.lift = /hive/data/genomes/hg38/hg38.contigs.lift braNey38.hapRegions = /hive/data/genomes/hg38/jkStuff/hg38.haplotypes.psl braNey38.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} braNey38.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} braNey38.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} braNey38.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} braNey38.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} braNey38.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} #braNey38.genbank.mrna.xeno.load = yes #braNey38.genbank.est.xeno.load = yes braNey38.refseq.mrna.xeno.load = yes braNey38.refseq.mrna.xeno.loadDesc = yes #braNey38.mgc = yes #braNey38.orfeome = yes #braNey38.downloadDir = hg38 braNey38.ccds.buildId = 20 # hg38.upstreamGeneTbl = refGene # hg38.upstreamMaf = multiz46way /hive/data/genomes/hg38/bed/multiz46way/species.list braNey38.genbank.mrna.blatTargetDb = yes braNey38.perChromTables = no # grcHhh38 - ANGIE TEST GRCh38 - Genome Reference Consortium Human Reference 38 # Assembly Accession: GCA_000001405.1 grcHhh38.serverGenome = /hive/data/genomes/grcHhh38/grcHhh38.2bit grcHhh38.ooc = /hive/data/genomes/grcHhh38/jkStuff/grcHhh38.11.ooc grcHhh38.lift = /hive/data/genomes/grcHhh38/jkStuff/grcHhh38.contigs.lift #grcHhh38.hapRegions = /hive/data/genomes/grcHhh38/jkStuff/grcHhh38.haplotypes.psl #grcHhh38.hapRegions = /hive/data/genomes/grcHhh38/jkStuff/grcHhh38.p11.alt.psl grcHhh38.hapRegions = /hive/data/genomes/grcHhh38/jkStuff/grcHhh38.p12.alt.psl grcHhh38.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} grcHhh38.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} grcHhh38.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} grcHhh38.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} grcHhh38.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} grcHhh38.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} #grcHhh38.genbank.mrna.xeno.load = yes #grcHhh38.genbank.est.xeno.load = yes grcHhh38.refseq.mrna.xeno.load = yes grcHhh38.refseq.mrna.xeno.loadDesc = yes #grcHhh38.mgc = yes #grcHhh38.orfeome = yes #grcHhh38.downloadDir = grcHhh38 #grcHhh38.ccds.buildId = 20 # grcHhh38.upstreamGeneTbl = refGene # grcHhh38.upstreamMaf = multiz46way /hive/data/genomes/grcHhh38/bed/multiz46way/species.list grcHhh38.genbank.mrna.blatTargetDb = yes grcHhh38.perChromTables = no # hg38 - GRCh38 - Genome Reference Consortium Human Reference 38 # Assembly Accession: GCA_000001405.1 hg38.serverGenome = /hive/data/genomes/hg38/hg38.2bit hg38.ooc = /hive/data/genomes/hg38/hg38.11.ooc hg38.lift = /hive/data/genomes/hg38/hg38.contigs.lift hg38.hapRegions = /hive/data/genomes/hg38/jkStuff/hg38.p12.alt.psl hg38.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} hg38.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} hg38.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} hg38.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} hg38.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} hg38.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} hg38.genbank.mrna.xeno.load = yes hg38.genbank.mrna.xeno.loadDesc = yes hg38.genbank.est.xeno.load = yes hg38.refseq.mrna.xeno.load = yes hg38.refseq.mrna.xeno.loadDesc = yes hg38.mgc = yes hg38.orfeome = yes hg38.downloadDir = hg38 hg38.ccds.buildId = 20 hg38.upstreamGeneTbl = refGene # hg38.upstreamMaf = multiz46way /hive/data/genomes/hg38/bed/multiz46way/species.list hg38.genbank.mrna.blatTargetDb = yes hg38.perChromTables = no # hg19 - GRCh37 - Genome Reference Consortium Human Reference 37 # Assembly Accession: GCA_000001405.1 #hg19.serverGenome = /hive/data/genomes/hg19/hg19.2bit hg19.serverGenome = /hive/data/genomes/hg19/hg19.initial.2bit hg19.ooc = /hive/data/genomes/hg19/11.ooc hg19.lift = /hive/data/genomes/hg19/jkStuff/hg19.unBridged.lift #hg19.hapRegions = /hive/data/genomes/hg19/jkStuff/hg19.p13.alt.psl hg19.hapRegions = /hive/data/genomes/hg19/jkStuff/hg19.haplotypes.psl hg19.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} hg19.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} hg19.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} hg19.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} hg19.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} hg19.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} hg19.genbank.mrna.xeno.load = yes hg19.genbank.est.xeno.load = yes hg19.refseq.mrna.xeno.load = yes hg19.refseq.mrna.xeno.loadDesc = yes hg19.mgc = yes hg19.orfeome = yes hg19.downloadDir = hg19 hg19.ccds.buildId = 15 hg19.upstreamGeneTbl = refGene hg19.upstreamMaf = multiz46way /hive/data/genomes/hg19/bed/multiz46way/species.list hg19.genbank.mrna.blatTargetDb = yes hg19.perChromTables = no # CHM1 - alternative Human assembly # refseq use less stringent filtering to annotate duplications CHM1.serverGenome = /hive/data/genomes/CHM1/CHM1.2bit CHM1.ooc = /hive/data/genomes/CHM1/11.ooc CHM1.lift = /hive/data/genomes/CHM1/jkStuff/CHM1.unBridged.lift CHM1.refseq.mrna.native.pslCDnaFilter = -minId=0.95 -minCover=0.25 -localNearBest=0.010 ${common.refseq.mrna.native.pslCDnaFilter} CHM1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} CHM1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} CHM1.genbank.mrna.native.load = yes CHM1.genbank.mrna.xeno.load = no CHM1.genbank.est.native.load = yes CHM1.genbank.est.xeno.load = no CHM1.refseq.mrna.native.load = yes CHM1.refseq.mrna.xeno.load = no CHM1.downloadDir = CHM1 CHM1.perChromTables = no # regenCho1 (Cricetulus griseus - Chinese hamster ovary cell line CHO-K1) regenCho1.serverGenome = /hive/data/genomes/regenCho1/regenCho1.2bit regenCho1.ooc = /hive/data/genomes/regenCho1/jkStuff/regenCho1.11.ooc regenCho1.lift = /hive/data/genomes/regenCho1/jkStuff/nonBridged.lift regenCho1.downloadDir = regenCho1 regenCho1.perChromTables = no regenCho1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} regenCho1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} regenCho1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} regenCho1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} regenCho1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc # regenCho1.upstreamGeneTbl = ensGene # regenCho1.upstreamMaf = multiz9way /hive/data/genomes/regenCho1/bed/multiz9way/species.list # criGriChoV2 (Cricetulus griseus - Chinese hamster ovary cell line CHO-K1) criGriChoV2.serverGenome = /hive/data/genomes/criGriChoV2/criGriChoV2.2bit criGriChoV2.ooc = /hive/data/genomes/criGriChoV2/jkStuff/criGriChoV2.11.ooc criGriChoV2.lift = no criGriChoV2.downloadDir = criGriChoV2 criGriChoV2.perChromTables = no criGriChoV2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} criGriChoV2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} criGriChoV2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} criGriChoV2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} criGriChoV2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc # criGriChoV2.upstreamGeneTbl = ensGene # criGriChoV2.upstreamMaf = multiz9way /hive/data/genomes/criGriChoV2/bed/multiz9way/species.list # criGriChoV1 (Cricetulus griseus - Chinese hamster ovary cell line CHO-K1) criGriChoV1.serverGenome = /hive/data/genomes/criGriChoV1/criGriChoV1.2bit criGriChoV1.ooc = /hive/data/genomes/criGriChoV1/jkStuff/criGriChoV1.11.ooc criGriChoV1.lift = no criGriChoV1.downloadDir = criGriChoV1 criGriChoV1.perChromTables = no criGriChoV1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} criGriChoV1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} criGriChoV1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} criGriChoV1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} criGriChoV1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc # criGriChoV1.upstreamGeneTbl = ensGene # criGriChoV1.upstreamMaf = multiz9way /hive/data/genomes/criGriChoV1/bed/multiz9way/species.list # criGri1 (Chinese hamster) criGri1.serverGenome = /hive/data/genomes/criGri1/criGri1.2bit criGri1.ooc = /hive/data/genomes/criGri1/jkStuff/criGri1.11.ooc criGri1.lift = no criGri1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} criGri1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} criGri1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} criGri1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} criGri1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} criGri1.refseq.mrna.native.load = yes criGri1.refseq.mrna.xeno.load = yes criGri1.genbank.mrna.xeno.load = no criGri1.genbank.est.native.load = yes criGri1.genbank.mrna.native.load = yes criGri1.genbank.mrna.native.loadDesc = no criGri1.downloadDir = criGri1 criGri1.perChromTables = no # aotNan1 (Ma's night monkey / Aotus nancymaae / taxId 37293) aotNan1.serverGenome = /hive/data/genomes/aotNan1/aotNan1.2bit aotNan1.ooc = /hive/data/genomes/aotNan1/jkStuff/aotNan1.11.ooc aotNan1.lift = no aotNan1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} aotNan1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} aotNan1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} aotNan1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} aotNan1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} aotNan1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} aotNan1.downloadDir = aotNan1 aotNan1.refseq.mrna.native.load = yes aotNan1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse aotNan1.genbank.mrna.xeno.load = no aotNan1.genbank.mrna.native.load = no aotNan1.genbank.est.native.load = no aotNan1.perChromTables = no # cebCap1 (White-faced sapajou - Cebus capucinus imitator) taxId 1737458 cebCap1.serverGenome = /hive/data/genomes/cebCap1/cebCap1.2bit cebCap1.ooc = /hive/data/genomes/cebCap1/jkStuff/cebCap1.11.ooc cebCap1.lift = no cebCap1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} cebCap1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} cebCap1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} cebCap1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} cebCap1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} cebCap1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} cebCap1.downloadDir = cebCap1 cebCap1.refseq.mrna.native.load = yes cebCap1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse cebCap1.genbank.mrna.xeno.load = no cebCap1.genbank.mrna.native.load = no cebCap1.genbank.est.native.load = no cebCap1.perChromTables = no # cerAty1 (Sooty mangabey - Cercocebus atys) taxId 9531 cerAty1.serverGenome = /hive/data/genomes/cerAty1/cerAty1.2bit cerAty1.ooc = /hive/data/genomes/cerAty1/jkStuff/cerAty1.11.ooc cerAty1.lift = no cerAty1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} cerAty1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} cerAty1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} cerAty1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} cerAty1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} cerAty1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} cerAty1.downloadDir = cerAty1 cerAty1.refseq.mrna.native.load = yes cerAty1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse cerAty1.genbank.mrna.xeno.load = no cerAty1.genbank.mrna.native.load = no cerAty1.genbank.est.native.load = no cerAty1.perChromTables = no # manLeu1 (Drill - Mandrillus leucophaeus) taxId 9568 manLeu1.serverGenome = /hive/data/genomes/manLeu1/manLeu1.2bit manLeu1.ooc = /hive/data/genomes/manLeu1/jkStuff/manLeu1.11.ooc manLeu1.lift = no manLeu1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} manLeu1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} manLeu1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} manLeu1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} manLeu1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} manLeu1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} manLeu1.downloadDir = manLeu1 manLeu1.refseq.mrna.native.load = yes manLeu1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse manLeu1.genbank.mrna.xeno.load = no manLeu1.genbank.mrna.native.load = no manLeu1.genbank.est.native.load = no manLeu1.perChromTables = no # neoSch1 (Hawaiian monk seal - Neomonachus schauinslandi) taxId 29088 neoSch1.serverGenome = /hive/data/genomes/neoSch1/neoSch1.2bit neoSch1.ooc = /hive/data/genomes/neoSch1/jkStuff/neoSch1.11.ooc neoSch1.lift = no neoSch1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} neoSch1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} neoSch1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} neoSch1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} neoSch1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} neoSch1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} neoSch1.downloadDir = neoSch1 neoSch1.refseq.mrna.native.load = no neoSch1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse neoSch1.genbank.mrna.xeno.load = no neoSch1.genbank.mrna.native.load = no neoSch1.genbank.est.native.load = no neoSch1.perChromTables = no # proCoq1 (Coquerel's sifaka - Propithecus coquereli) taxId 379532 proCoq1.serverGenome = /hive/data/genomes/proCoq1/proCoq1.2bit proCoq1.ooc = /hive/data/genomes/proCoq1/jkStuff/proCoq1.11.ooc proCoq1.lift = no proCoq1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} proCoq1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} proCoq1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} proCoq1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} proCoq1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} proCoq1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} proCoq1.downloadDir = proCoq1 proCoq1.refseq.mrna.native.load = yes proCoq1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse proCoq1.genbank.mrna.xeno.load = no proCoq1.genbank.mrna.native.load = no proCoq1.genbank.est.native.load = no proCoq1.perChromTables = no # mm7 mm7.serverGenome = /hive/data/genomes/mm7/mm7.2bit mm7.ooc = /hive/data/genomes/mm7/11.ooc mm7.align.unplacedChroms = chrUn_random mm7.lift = /hive/data/genomes/mm7/jkStuff/liftAll.lft mm7.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} mm7.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} mm7.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} mm7.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} mm7.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} mm7.downloadDir = mm7 mm7.refseq.mrna.xeno.load = yes mm7.refseq.mrna.xeno.loadDesc = yes mm7.genbank.mrna.xeno.load = yes mm7.mgc = yes mm7.upstreamGeneTbl = refGene mm7.upstreamMaf = multiz17way /hive/data/genomes/mm7/bed/multiz17way/species.lst # mm8 mm8.serverGenome = /hive/data/genomes/mm8/mm8.2bit mm8.ooc = /hive/data/genomes/mm8/11.ooc mm8.align.unplacedChroms = chrUn_random mm8.lift = /hive/data/genomes/mm8/jkStuff/liftAll.lft mm8.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} mm8.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} mm8.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} mm8.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} mm8.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} mm8.downloadDir = mm8 mm8.refseq.mrna.xeno.load = yes mm8.refseq.mrna.xeno.loadDesc = yes mm8.genbank.mrna.xeno.load = yes mm8.mgc = yes mm8.upstreamGeneTbl = refGene mm8.upstreamMaf = multiz17way /hive/data/genomes/mm8/bed/multiz17way/species.lst # mm9 mm9.serverGenome = /hive/data/genomes/mm9/mm9.2bit mm9.ooc = /hive/data/genomes/mm9/11.ooc mm9.align.unplacedChroms = *_random mm9.lift = /hive/data/genomes/mm9/jkStuff/nonBridgedGap.lft mm9.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} mm9.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} mm9.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} mm9.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} mm9.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} mm9.downloadDir = mm9 mm9.refseq.mrna.xeno.load = yes mm9.refseq.mrna.xeno.loadDesc = yes mm9.genbank.mrna.xeno.load = yes mm9.mgc = yes mm9.orfeome = yes mm9.ccds.buildId = 7 mm9.upstreamGeneTbl = refGene mm9.upstreamMaf = multiz30way /hive/data/genomes/mm9/bed/multiz30way/species.list mm9.genbank.mrna.blatTargetDb = yes # GRCm38B GRCm38B.serverGenome = /hive/data/genomes/GRCm38B/GRCm38B.2bit GRCm38B.ooc = /hive/data/genomes/GRCm38B/jkStuff/GRCm38B.11.ooc GRCm38B.lift = /hive/data/genomes/GRCm38B/jkStuff/GRCm38B.nonBridged.lft GRCm38B.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} GRCm38B.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} GRCm38B.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} GRCm38B.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} GRCm38B.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} GRCm38B.downloadDir = GRCm38B GRCm38B.refseq.mrna.xeno.load = yes GRCm38B.refseq.mrna.xeno.loadDesc = yes GRCm38B.genbank.mrna.xeno.load = yes #GRCm38B.mgc = yes #GRCm38B.orfeome = yes #GRCm38B.ccds.buildId = 21 #GRCm38B.genbank.mrna.blatTargetDb = yes # GRCm38B.upstreamGeneTbl = refGene # GRCm38B.upstreamMaf = multiz60way /hive/data/genomes/GRCm38B/bed/multiz60way/species.list # mm39 - (house mouse - GCA_000001635.9 - GRCm39) mm39.serverGenome = /hive/data/genomes/mm39/mm39.2bit mm39.ooc = /hive/data/genomes/mm39/jkStuff/mm39.11.ooc mm39.lift = /hive/data/genomes/mm39/jkStuff/mm39.5Kgaps.lft mm39.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} mm39.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} mm39.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} mm39.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} mm39.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} mm39.downloadDir = mm39 mm39.refseq.mrna.xeno.load = yes mm39.refseq.mrna.xeno.loadDesc = yes mm39.genbank.mrna.xeno.load = yes mm39.genbank.mrna.blatTargetDb = yes mm39.upstreamGeneTbl = refGene # mm39.mgc = yes # mm39.orfeome = yes # mm39.ccds.buildId = 21 # mm39.upstreamMaf = multiz60way /hive/data/genomes/mm39/bed/multiz60way/species.list # mm10 mm10.serverGenome = /hive/data/genomes/mm10/mm10.2bit mm10.ooc = /hive/data/genomes/mm10/mm10.11.ooc mm10.lift = /hive/data/genomes/mm10/mm10.nonBridged.lift mm10.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} mm10.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} mm10.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} mm10.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} mm10.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} mm10.downloadDir = mm10 mm10.refseq.mrna.xeno.load = yes mm10.refseq.mrna.xeno.loadDesc = yes mm10.genbank.mrna.xeno.load = yes mm10.mgc = yes mm10.orfeome = yes mm10.ccds.buildId = 21 mm10.genbank.mrna.blatTargetDb = yes mm10.upstreamGeneTbl = refGene mm10.upstreamMaf = multiz60way /hive/data/genomes/mm10/bed/multiz60way/species.list # rn3 rn3.serverGenome = /hive/data/genomes/rn3/rn3.2bit rn3.ooc = /hive/data/genomes/rn3/11.ooc rn3.align.unplacedChroms = chrUn,chrUn_random rn3.lift = /hive/data/genomes/rn3/jkStuff/liftAll.lft rn3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} rn3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} rn3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} rn3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} rn3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} rn3.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} #rn3.genbank.mrna.xeno.load = yes rn3.downloadDir = rnJun2003 rn3.refseq.mrna.xeno.load = yes rn3.mgc = yes rn3.upstreamGeneTbl = refGene # rn4 rn4.serverGenome = /hive/data/genomes/rn4/rn4.2bit rn4.ooc = /hive/data/genomes/rn4/11.ooc rn4.align.unplacedChroms = chrUn,chr*_random rn4.lift = /hive/data/genomes/rn4/jkStuff/liftAll.lft rn4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} rn4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} rn4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} rn4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} rn4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} rn4.downloadDir = rn4 rn4.refseq.mrna.xeno.load = yes rn4.refseq.mrna.xeno.loadDesc = yes rn4.genbank.mrna.xeno.load = yes rn4.mgc = yes rn4.upstreamGeneTbl = refGene rn4.upstreamMaf = multiz9way /hive/data/genomes/rn4/bed/multiz9way/species.lst # rn5 (rat) rn5.serverGenome = /hive/data/genomes/rn5/rn5.2bit rn5.ooc = /hive/data/genomes/rn5/jkStuff/rn5.11.ooc rn5.lift = /hive/data/genomes/rn5/jkStuff/rn5.nonBridged.lift rn5.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} rn5.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} rn5.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} rn5.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} rn5.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} rn5.downloadDir = rn5 rn5.refseq.mrna.xeno.load = yes rn5.refseq.mrna.xeno.loadDesc = yes rn5.genbank.mrna.xeno.load = yes rn5.perChromTables = no rn5.mgc = yes rn5.upstreamGeneTbl = ensGene rn5.upstreamMaf = multiz13way /hive/data/genomes/rn5/bed/multiz13way/species.list.txt # regenRn1 (Regeneron rat assembly) regenRn1.serverGenome = /hive/data/genomes/regenRn1/regenRn1.2bit regenRn1.ooc = /hive/data/genomes/regenRn1/jkStuff/regenRn1.11.ooc regenRn1.lift = /hive/data/genomes/regenRn1/jkStuff/nonBridged.lift regenRn1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} regenRn1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} regenRn1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} regenRn1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} regenRn1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} regenRn1.downloadDir = regenRn1 regenRn1.refseq.mrna.xeno.load = yes regenRn1.refseq.mrna.xeno.loadDesc = yes regenRn1.genbank.mrna.xeno.load = yes regenRn1.perChromTables = no regenRn1.mgc = yes # regenRn1.upstreamGeneTbl = ensGene # regenRn1.upstreamMaf = multiz13way /hive/data/genomes/regenRn1/bed/multiz13way/species.list.txt # regenRn0 (Regeneron rat assembly) regenRn0.serverGenome = /hive/data/genomes/regenRn0/regenRn0.2bit regenRn0.ooc = /hive/data/genomes/regenRn0/jkStuff/regenRn0.11.ooc regenRn0.lift = /hive/data/genomes/regenRn0/jkStuff/nonBridged.lift regenRn0.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} regenRn0.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} regenRn0.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} regenRn0.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} regenRn0.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} regenRn0.downloadDir = regenRn0 regenRn0.refseq.mrna.xeno.load = yes regenRn0.refseq.mrna.xeno.loadDesc = yes regenRn0.genbank.mrna.xeno.load = yes regenRn0.perChromTables = no regenRn0.mgc = yes # regenRn0.upstreamGeneTbl = ensGene # regenRn0.upstreamMaf = multiz13way /hive/data/genomes/regenRn0/bed/multiz13way/species.list.txt # rn6 (rat) rn6.serverGenome = /hive/data/genomes/rn6/rn6.2bit rn6.ooc = /hive/data/genomes/rn6/jkStuff/rn6.11.ooc rn6.lift = /hive/data/genomes/rn6/jkStuff/rn6.nonBridged.lift rn6.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} rn6.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} rn6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} rn6.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} rn6.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} rn6.downloadDir = rn6 rn6.refseq.mrna.xeno.load = yes rn6.refseq.mrna.xeno.loadDesc = yes rn6.genbank.mrna.xeno.load = yes rn6.perChromTables = no rn6.mgc = yes # rn6.upstreamGeneTbl = ensGene # rn6.upstreamMaf = multiz13way /hive/data/genomes/rn6/bed/multiz13way/species.list.txt # micOch1 (prairie vole) micOch1.serverGenome = /hive/data/genomes/micOch1/micOch1.2bit micOch1.ooc = /hive/data/genomes/micOch1/jkStuff/micOch1.11.ooc micOch1.lift = /hive/data/genomes/micOch1/jkStuff/nonBridged.lft micOch1.perChromTables = no micOch1.downloadDir = micOch1 micOch1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} micOch1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} micOch1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} micOch1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} micOch1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults are fine: genbank.mrna.native refseq.mrna.native refseq.mrna.xeno yes # and genbank.est.native # there is no multiple alignment yet: # micOch1.upstreamGeneTbl = refGene # micOch1.upstreamMaf = multiz7way # /hive/data/genomes/micOch1/bed/multiz7way/species.lst # fukDam1 - Fukomys damarensis (Damara mole-rat) fukDam1.serverGenome = /hive/data/genomes/fukDam1/fukDam1.2bit fukDam1.ooc = /hive/data/fukDam1/jkStuff/fukDam1.11.ooc fukDam1.lift = no fukDam1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} fukDam1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} fukDam1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} fukDam1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} fukDam1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} fukDam1.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} fukDam1.refseq.mrna.native.load = yes fukDam1.refseq.mrna.xeno.load = yes fukDam1.genbank.mrna.native.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse fukDam1.genbank.mrna.xeno.load = yes fukDam1.genbank.est.native.load = no fukDam1.downloadDir = fukDam1 fukDam1.perChromTables = no # hetGla2 (moleRat) hetGla2.serverGenome = /hive/data/genomes/hetGla2/hetGla2.2bit hetGla2.ooc = /hive/data/hetGla2/jkStuff/hetGla2.11.ooc hetGla2.lift = no hetGla2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} hetGla2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} hetGla2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} hetGla2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} hetGla2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} hetGla2.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} hetGla2.refseq.mrna.native.load = no hetGla2.refseq.mrna.xeno.load = yes hetGla2.genbank.mrna.native.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse hetGla2.genbank.mrna.xeno.load = yes hetGla2.genbank.est.native.load = no hetGla2.downloadDir = hetGla2 hetGla2.perChromTables = no # hetGla1 (moleRat) hetGla1.serverGenome = /hive/data/genomes/hetGla1/hetGla1.2bit hetGla1.ooc = /hive/data/genomes/hetGla1/hetGla1.11.ooc hetGla1.lift = no hetGla1.perChromTables = no hetGla1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} hetGla1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} hetGla1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} hetGla1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} hetGla1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} hetGla1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} hetGla1.downloadDir = hetGla1 hetGla1.refseq.mrna.native.load = no hetGla1.refseq.mrna.xeno.load = yes hetGla1.refseq.mrna.xeno.loadDesc = yes hetGla1.genbank.mrna.native.load = yes hetGla1.genbank.mrna.native.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse hetGla1.genbank.mrna.xeno.load = yes hetGla1.genbank.mrna.xeno.loadDesc = yes hetGla1.genbank.est.native.load = yes hetGla1.genbank.est.native.loadDesc = yes # sarHar1 (Tasmanian Devil) sarHar1.serverGenome = /hive/data/genomes/sarHar1/sarHar1.2bit sarHar1.ooc = /hive/data/genomes/sarHar1/sarHar1.11.ooc sarHar1.lift = no sarHar1.perChromTables = no sarHar1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} sarHar1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} sarHar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} sarHar1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} sarHar1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} sarHar1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} sarHar1.downloadDir = sarHar1 sarHar1.refSeq.native.load = no sarHar1.refseq.mrna.xeno.load = yes sarHar1.refseq.mrna.xeno.loadDesc = yes sarHar1.genbank.mrna.native.load = yes sarHar1.genbank.mrna.native.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse sarHar1.genbank.est.native.load = no sarHar1.genbank.est.native.loadDesc = no # fr1 fr1.serverGenome = /hive/data/genomes/fr1/fr1.2bit fr1.ooc = no fr1.align.unplacedChroms = chrUn fr1.lift = /hive/data/genomes/fr1/Un/chrUn-frag.lft fr1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} fr1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} fr1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} fr1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} fr1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} fr1.genbank.mrna.xeno.loadDesc = yes fr1.refseq.mrna.native.load = no fr1.refseq.mrna.xeno.load = no fr1.upstreamGeneTbl = ensGene # fr2 fr2.serverGenome = /hive/data/genomes/fr2/fr2.2bit fr2.ooc = /hive/data/genomes/fr2/11.ooc fr2.align.unplacedChroms = chrUn fr2.lift = /hive/data/genomes/fr2/jkStuff/liftAll.lft fr2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} fr2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} fr2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} fr2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} fr2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} fr2.genbank.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse fr2.genbank.mrna.xeno.load = yes fr2.refseq.mrna.native.load = no fr2.refseq.mrna.xeno.load = no fr2.upstreamGeneTbl = ensGene fr2.upstreamMaf = multiz5way /hive/data/genomes/fr2/bed/multiz5way/species.lst # fr3 fr3.serverGenome = /hive/data/genomes/fr3/fr3.2bit fr3.ooc = /hive/data/genomes/fr3/fr3.11.ooc # fr3.lift = /hive/data/genomes/fr3/fr3.nonBridged.lift fr3.perChromTables = no fr3.lift = no fr3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} fr3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} fr3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} fr3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} fr3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} fr3.genbank.mrna.xeno.loadDesc = yes fr3.refseq.mrna.xeno.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse fr3.genbank.mrna.xeno.load = yes fr3.upstreamGeneTbl = ensGene fr3.upstreamMaf = multiz8way /hive/data/genomes/fr3/bed/multiz8way/species.list # dm1 dm1.serverGenome = /hive/data/genomes/dm1/nib/chr*.nib dm1.ooc = /hive/data/genomes/dm1/11.ooc dm1.lift = /hive/data/genomes/dm1/jkStuff/liftAll.lft dm1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} dm1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} dm1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} dm1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} dm1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse dm1.downloadDir = dm1 # dm2 (D. melanogaster) dm2.serverGenome = /hive/data/genomes/dm2/nib/chr*.nib dm2.ooc = /hive/data/genomes/dm1/11.ooc dm2.lift = /hive/data/genomes/dm2/jkStuff/liftAll.lft dm2.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} dm2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} dm2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} dm2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} dm2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse dm2.genbank.mrna.xeno.load = yes dm2.downloadDir = dm2 dm2.upstreamGeneTbl = refGene dm2.upstreamMaf = multiz15way /hive/data/genomes/dm2/bed/multiz15way/species.lst # dm6 (D. melanogaster) dm6.serverGenome = /hive/data/genomes/dm6/dm6.2bit dm6.ooc = /hive/data/genomes/dm6/jkStuff/dm6.11.ooc dm6.lift = no dm6.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} dm6.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} dm6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} dm6.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} dm6.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse dm6.genbank.mrna.xeno.load = yes dm6.perChromTables = no dm6.upstreamGeneTbl = refGene dm6.upstreamMaf = multiz27way /hive/data/genomes/dm6/bed/multiz27way/species.list.txt # dm3 (D. melanogaster) dm3.serverGenome = /hive/data/genomes/dm3/dm3.2bit dm3.ooc = /hive/data/genomes/dm3/11.ooc dm3.lift = /hive/data/genomes/dm3/jkStuff/liftAll.lft dm3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} dm3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} dm3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} dm3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} dm3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse dm3.genbank.mrna.xeno.load = yes dm3.upstreamGeneTbl = refGene dm3.upstreamMaf = multiz15way /hive/data/genomes/dm3/bed/multiz15way/species.lst # sacCer3 S. cerevisiae sacCer3.serverGenome = /hive/data/genomes/sacCer3/sacCer3.2bit sacCer3.ooc = no sacCer3.maxIntron = 5000 sacCer3.lift = no sacCer3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} sacCer3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} sacCer3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} sacCer3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} sacCer3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} #sacCer3.perChromTables = no # doesn't work in the browser sacCer3.genbank.mrna.xeno.load = no sacCer3.refseq.mrna.native.load = no sacCer3.downloadDir = sacCer3 sacCer3.upstreamGeneTbl = xenoRefGene sacCer3.upstreamMaf = multiz7way /hive/data/genomes/sacCer3/bed/multiz7way/species.lst # sacCer2 S. cerevisiae sacCer2.serverGenome = /hive/data/genomes/sacCer2/sacCer2.2bit sacCer2.ooc = no sacCer2.maxIntron = 5000 sacCer2.lift = no sacCer2.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} sacCer2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} sacCer2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} sacCer2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} sacCer2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} #sacCer2.perChromTables = no # doesn't work in the browser sacCer2.genbank.mrna.xeno.load = no sacCer2.refseq.mrna.native.load = no sacCer2.downloadDir = sacCer2 sacCer2.upstreamGeneTbl = xenoRefGene sacCer2.upstreamMaf = multiz7way /hive/data/genomes/sacCer2/bed/multiz7way/species.list # sacCer1 sacCer1.serverGenome = /hive/data/genomes/sacCer1/nib/chr*.nib sacCer1.ooc = no sacCer1.maxIntron = 5000 sacCer1.lift = no sacCer1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} sacCer1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} sacCer1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} sacCer1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} sacCer1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} #sacCer1.perChromTables = no # doesn't work in the browser sacCer1.genbank.mrna.xeno.load = no sacCer1.refseq.mrna.native.load = no sacCer1.downloadDir = sacCer1 # panPan3 (bonobo - Pan paniscus - GCF_013052645.1 Mhudiblu_PPA_v0 15 May 2020) panPan3.serverGenome = /hive/data/genomes/panPan3/panPan3.2bit panPan3.ooc = /hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc panPan3.lift = /hive/data/genomes/panPan3/jkStuff/panPan3.nonBridged.lft panPan3.perChromTables = no panPan3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} panPan3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} panPan3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} panPan3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} panPan3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} panPan3.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} panPan3.downloadDir = panPan3 # defaults yes genbank.mrna.native, genbank.est.native.load, # refseq.mrna.native, refseq.mrna.xeno # DO NOT NEED genbank.mrna.xeno except for human, mouse panPan3.genbank.est.native.load = no # panPan2 (bonobo - Pan paniscus) panPan2.serverGenome = /hive/data/genomes/panPan2/panPan2.2bit panPan2.ooc = /hive/data/genomes/panPan2/jkStuff/panPan2.11.ooc panPan2.lift = /hive/data/genomes/panPan2/jkStuff/panPan2.nonBridged.lft panPan2.perChromTables = no panPan2.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} panPan2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} panPan2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} panPan2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} panPan2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} panPan2.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} panPan2.downloadDir = panPan2 # defaults yes genbank.mrna.native, genbank.est.native.load, # refseq.mrna.native, refseq.mrna.xeno # DO NOT NEED genbank.mrna.xeno except for human, mouse panPan2.genbank.est.native.load = no # panPan1 (bonobo) panPan1.serverGenome = /hive/data/genomes/panPan1/panPan1.2bit panPan1.ooc = /hive/data/genomes/panPan1/jkStuff/panPan1.11.ooc panPan1.lift = no panPan1.perChromTables = no panPan1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} panPan1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} panPan1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} panPan1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} panPan1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} panPan1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} panPan1.downloadDir = panPan1 panPan1.refseq.mrna.native.load = yes panPan1.refseq.mrna.native.loadDesc = yes panPan1.refseq.mrna.xeno.load = yes panPan1.refseq.mrna.xeno.loadDesc = yes panPan1.genbank.mrna.native.load = yes panPan1.genbank.mrna.native.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse panPan1.genbank.mrna.xeno.load = no panPan1.genbank.est.native.load = no # panTro6 (chimp - Pan troglodytes - refseq GCF_002880755.1 - taxId 9598) panTro6.serverGenome = /hive/data/genomes/panTro6/panTro6.2bit panTro6.ooc = /hive/data/genomes/panTro6/jkStuff/panTro6.11.ooc panTro6.lift = /hive/data/genomes/panTro6/jkStuff/panTro6.nonBridged.lft panTro6.perChromTables = no panTro6.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} panTro6.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} panTro6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} panTro6.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} panTro6.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} panTro6.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} panTro6.downloadDir = panTro6 # defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc # yes: genbank.est.native.load refseq.mrna.native.load # yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load # yes: refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc # no: genbank.est.native.loadDesc genbank.est.xeno.load # no: genbank.est.xeno.loadDesc # DO NOT NEED genbank.mrna.xeno except for human, mouse # have been doing this for chimp too: panTro6.genbank.mrna.xeno.load = yes # panTro5 (chimp) panTro5.serverGenome = /hive/data/genomes/panTro5/panTro5.2bit panTro5.ooc = /hive/data/genomes/panTro5/jkStuff/panTro5.11.ooc panTro5.lift = /hive/data/genomes/panTro5/jkStuff/nonBridged.lft panTro5.perChromTables = no panTro5.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} panTro5.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} panTro5.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} panTro5.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} panTro5.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} panTro5.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} panTro5.downloadDir = panTro5 panTro5.refseq.mrna.native.load = yes panTro5.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse panTro5.genbank.mrna.xeno.load = yes # panTro5.upstreamGeneTbl = ensGene # panTro5.upstreamMaf = multiz12way /hive/data/genomes/panTro5/bed/multiz12way/species.list # panTro4 (chimp) panTro4.serverGenome = /hive/data/genomes/panTro4/panTro4.2bit panTro4.ooc = /hive/data/genomes/panTro4/jkStuff/panTro4.11.ooc panTro4.lift = /hive/data/genomes/panTro4/jkStuff/panTro4.nonBridged.lift panTro4.perChromTables = no panTro4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} panTro4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} panTro4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} panTro4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} panTro4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} panTro4.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} panTro4.downloadDir = panTro4 panTro4.refseq.mrna.native.load = yes panTro4.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse panTro4.genbank.mrna.xeno.load = yes panTro4.genbank.mrna.xeno.loadDesc = yes panTro4.genbank.est.native.load = yes # panTro4.upstreamGeneTbl = ensGene # panTro4.upstreamMaf = multiz12way /hive/data/genomes/panTro4/bed/multiz12way/species.list # chimp panTro3.serverGenome = /hive/data/genomes/panTro3/panTro3.2bit panTro3.ooc = /hive/data/genomes/panTro3/panTro3.11.ooc panTro3.align.unplacedChroms = chrUn*,chr*_random panTro3.lift = /hive/data/genomes/panTro3/panTro3.nonBridged.lft panTro3.perChromTables = no panTro3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} panTro3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} panTro3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} panTro3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} panTro3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} panTro3.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} panTro3.downloadDir = panTro3 panTro3.refseq.mrna.native.load = yes panTro3.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse panTro3.genbank.mrna.xeno.load = yes panTro3.genbank.mrna.xeno.loadDesc = yes panTro3.genbank.est.native.load = yes panTro3.upstreamGeneTbl = ensGene panTro3.upstreamMaf = multiz12way /hive/data/genomes/panTro3/bed/multiz12way/species.list panTro1.serverGenome = /hive/data/genomes/panTro1/panTro1.2bit panTro1.ooc = /hive/data/genomes/panTro1/11.ooc panTro1.align.unplacedChroms = chrUn_random panTro1.lift = /hive/data/genomes/panTro1/jkStuff/liftAll.lft panTro1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} panTro1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} panTro1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} panTro1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} panTro1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} panTro1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} panTro1.downloadDir = panTro1 panTro1.refseq.mrna.native.load = yes panTro1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse panTro1.genbank.est.native.load = yes panTro1.upstreamGeneTbl = ensGene panTro2.serverGenome = /hive/data/genomes/panTro2/panTro2.2bit panTro2.ooc = /hive/data/genomes/panTro2/11.ooc panTro2.align.unplacedChroms = chrUn,chr*_random panTro2.lift = /hive/data/genomes/panTro2/lifts/genbank.lft panTro2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} panTro2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} panTro2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} panTro2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} panTro2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} panTro2.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} panTro2.downloadDir = panTro2 panTro2.refseq.mrna.native.load = yes panTro2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse panTro2.genbank.mrna.xeno.load = yes panTro2.genbank.mrna.xeno.loadDesc = yes panTro2.genbank.est.native.load = yes panTro2.upstreamGeneTbl = refGene # Gorilla - refseq assembly: GCF_008122165.1 gorGor6.serverGenome = /hive/data/genomes/gorGor6/gorGor6.2bit gorGor6.ooc = /hive/data/genomes/gorGor6/jkStuff/gorGor6.11.ooc gorGor6.lift = /hive/data/genomes/gorGor6/jkStuff/gorGor6.nonBridged.lft gorGor6.perChromTables = no gorGor6.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} gorGor6.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} gorGor6.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} gorGor6.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} gorGor6.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} gorGor6.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} gorGor6.downloadDir = gorGor6 # default yes refseq.mrna.native refseq.mrna.xeno genbank.mrna.native # default yes genbank.est.native # default no genbank.mrna.xeno genbank.est.xeno # Gorilla gorGor5.serverGenome = /hive/data/genomes/gorGor5/gorGor5.2bit gorGor5.ooc = /hive/data/genomes/gorGor5/jkStuff/gorGor5.11.ooc gorGor5.lift = no gorGor5.perChromTables = no gorGor5.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} gorGor5.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} gorGor5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} gorGor5.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} gorGor5.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} gorGor5.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} gorGor5.downloadDir = gorGor5 # default yes refseq.mrna.native refseq.mrna.xeno genbank.mrna.native # default yes genbank.est.native # default no genbank.mrna.xeno genbank.est.xeno # Gorilla gorGor4.serverGenome = /hive/data/genomes/gorGor4/gorGor4.2bit gorGor4.ooc = /hive/data/genomes/gorGor4/jkStuff/gorGor4.11.ooc gorGor4.lift = /hive/data/genomes/gorGor4/jkStuff/gorGor4.nonBridged.lft gorGor4.perChromTables = no gorGor4.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} gorGor4.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} gorGor4.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} gorGor4.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} gorGor4.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} gorGor4.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} gorGor4.downloadDir = gorGor4 # refseq.mrna native and xeno are default yes # genbank.mrna and genbank.est native are default yes, the xeno is default no # reset upstream* if and when a multiple alignment is constructed # gorGor4.upstreamGeneTbl = ensGene # gorGor4.upstreamMaf = multiz11way /hive/data/genomes/gorGor4/bed/multiz11way/species.list # Gorilla gorGor3.serverGenome = /hive/data/genomes/gorGor3/gorGor3.2bit gorGor3.ooc = /hive/data/genomes/gorGor3/gorGor3.11.ooc gorGor3.lift = no gorGor3.perChromTables = no gorGor3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} gorGor3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} gorGor3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} gorGor3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} gorGor3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} gorGor3.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} gorGor3.downloadDir = gorGor3 gorGor3.refseq.mrna.native.load = no gorGor3.refseq.mrna.xeno.load = yes gorGor3.refseq.mrna.xeno.loadDesc = yes gorGor3.genbank.mrna.xeno.load = yes gorGor3.genbank.est.native.load = no gorGor3.upstreamGeneTbl = ensGene gorGor3.upstreamMaf = multiz11way /hive/data/genomes/gorGor3/bed/multiz11way/species.list # Baboon # papAnu4 (Papio anubis - olive baboon taxId: 9555) papAnu4.serverGenome = /hive/data/genomes/papAnu4/papAnu4.2bit papAnu4.ooc = /hive/data/genomes/papAnu4/jkStuff/papAnu4.11.ooc papAnu4.lift = /hive/data/genomes/papAnu4/jkStuff/nonBridged.lft papAnu4.perChromTables = no papAnu4.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} papAnu4.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} papAnu4.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} papAnu4.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} papAnu4.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} papAnu4.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} papAnu4.downloadDir = papAnu4 # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc # papAnu3 (baboon) papAnu3.serverGenome = /hive/data/genomes/papAnu3/papAnu3.2bit papAnu3.ooc = /hive/data/genomes/papAnu3/jkStuff/papAnu3.11.ooc papAnu3.lift = /hive/data/genomes/papAnu3/jkStuff/papAnu3.nonBridged.lft papAnu3.perChromTables = no papAnu3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} papAnu3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} papAnu3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} papAnu3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} papAnu3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} papAnu3.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} papAnu3.downloadDir = papAnu3 # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc # Baboon # papAnu2 (baboon) papAnu2.serverGenome = /hive/data/genomes/papAnu2/papAnu2.2bit papAnu2.ooc = /hive/data/genomes/papAnu2/jkStuff/papAnu2.11.ooc papAnu2.lift = /hive/data/genomes/papAnu2/jkStuff/papAnu2.nonBridged.lift papAnu2.perChromTables = no papAnu2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} papAnu2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} papAnu2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} papAnu2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} papAnu2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} papAnu2.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} papAnu2.downloadDir = papAnu2 papAnu2.refseq.mrna.native.load = yes papAnu2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse papAnu2.genbank.mrna.xeno.load = yes papAnu2.genbank.mrna.xeno.loadDesc = yes papAnu2.genbank.est.native.load = yes papHam1.serverGenome = /hive/data/genomes/papHam1/papHam1.2bit papHam1.ooc = /hive/data/genomes/papHam1/papHam1.11.ooc papHam1.lift = no papHam1.perChromTables = no papHam1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} papHam1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} papHam1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} papHam1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} papHam1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} papHam1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} papHam1.downloadDir = papHam1 papHam1.refseq.mrna.native.load = yes papHam1.refseq.mrna.xeno.load = yes papHam1.refseq.mrna.xeno.loadDesc = yes papHam1.genbank.est.native.load = no papHam1.upstreamGeneTbl = xenoRefGene # ponAbe3 (Orangutan - Pongo abelli - refseq GCF_002880775.1 - taxId 9601) ponAbe3.serverGenome = /hive/data/genomes/ponAbe3/ponAbe3.2bit ponAbe3.ooc = /hive/data/genomes/ponAbe3/jkStuff/ponAbe3.11.ooc ponAbe3.lift = /hive/data/genomes/ponAbe3/jkStuff/ponAbe3.nonBridged.lft ponAbe3.perChromTables = no ponAbe3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} ponAbe3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} ponAbe3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} ponAbe3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} ponAbe3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} ponAbe3.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} ponAbe3.downloadDir = ponAbe3 # defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc # yes: genbank.est.native.load refseq.mrna.native.load # yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load # yes: refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc # no: genbank.est.native.loadDesc genbank.est.xeno.load # no: genbank.est.xeno.loadDesc # DO NOT NEED genbank.mrna.xeno except for human, mouse # Orangutan ponAbe2.serverGenome = /hive/data/genomes/ponAbe2/ponAbe2.2bit ponAbe2.ooc = /hive/data/genomes/ponAbe2/11.ooc ponAbe2.align.unplacedChroms = chrUn,chr*_random ponAbe2.lift = /hive/data/genomes/ponAbe2/jkStuff/genbank.lft ponAbe2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} ponAbe2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} ponAbe2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} ponAbe2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} ponAbe2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} ponAbe2.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} ponAbe2.downloadDir = ponAbe2 ponAbe2.refseq.mrna.native.load = yes ponAbe2.refseq.mrna.xeno.load = yes ponAbe2.refseq.mrna.xeno.loadDesc = yes ponAbe2.genbank.mrna.xeno.load = yes ponAbe2.upstreamGeneTbl = xenoRefGene ponAbe2.upstreamMaf = multiz8way /hive/data/genomes/ponAbe2/bed/multiz8way/species.list # nomLeu3 (Gibbon) nomLeu3.serverGenome = /hive/data/genomes/nomLeu3/nomLeu3.2bit nomLeu3.ooc = /hive/data/genomes/nomLeu3/nomLeu3.11.ooc nomLeu3.lift = /hive/data/genomes/nomLeu3/jkStuff/nomLeu3.nonBridged.lift nomLeu3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} nomLeu3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} nomLeu3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} nomLeu3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} nomLeu3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} nomLeu3.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} nomLeu3.refseq.mrna.native.load = no nomLeu3.refseq.mrna.xeno.load = yes nomLeu3.genbank.mrna.native.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse nomLeu3.genbank.mrna.xeno.load = yes nomLeu3.genbank.est.native.load = no nomLeu3.downloadDir = nomLeu3 nomLeu3.perChromTables = no # nomLeu2 (Gibbon) nomLeu2.serverGenome = /hive/data/genomes/nomLeu2/nomLeu2.2bit nomLeu2.ooc = /hive/data/genomes/nomLeu2/nomLeu2.11.ooc nomLeu2.lift = no nomLeu2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} nomLeu2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} nomLeu2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} nomLeu2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} nomLeu2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} nomLeu2.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} nomLeu2.refseq.mrna.native.load = no nomLeu2.refseq.mrna.xeno.load = yes nomLeu2.genbank.mrna.native.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse nomLeu2.genbank.est.native.load = no nomLeu2.downloadDir = nomLeu2 nomLeu2.perChromTables = no # nomLeu1 (Gibbon) nomLeu1.serverGenome = /hive/data/genomes/nomLeu1/nomLeu1.2bit nomLeu1.ooc = /hive/data/genomes/nomLeu1/nomLeu1.11.ooc nomLeu1.lift = no nomLeu1.perChromTables = no nomLeu1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} nomLeu1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} nomLeu1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} nomLeu1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} nomLeu1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} nomLeu1.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} nomLeu1.downloadDir = nomLeu1 nomLeu1.refseq.mrna.native.load = no nomLeu1.refseq.mrna.xeno.load = yes nomLeu1.refseq.mrna.xeno.loadDesc = yes nomLeu1.genbank.mrna.native.load = yes nomLeu1.genbank.mrna.native.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse nomLeu1.genbank.est.native.load = no nomLeu1.genbank.est.native.loadDesc = no # macNem1 (pig-tailed macaque) macNem1.serverGenome = /hive/data/genomes/macNem1/macNem1.2bit macNem1.ooc = /hive/data/genomes/macNem1/jkStuff/macNem1.11.ooc macNem1.lift = no macNem1.perChromTables = no macNem1.downloadDir = macNem1 macNem1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} macNem1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} macNem1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} macNem1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} macNem1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults are fine: genbank.mrna.native refseq.mrna.native refseq.mrna.xeno yes # and genbank.est.native # macNem1.upstreamGeneTbl = refGene # macNem1.upstreamMaf = multiz7way # /hive/data/genomes/macNem1/bed/multiz7way/species.lst # macFas5 (Crab-eating macaque) macFas5.serverGenome = /hive/data/genomes/macFas5/macFas5.2bit macFas5.ooc = /hive/data/genomes/macFas5/jkStuff/macFas5.11.ooc macFas5.lift = /hive/data/genomes/macFas5/jkStuff/macFas5.nonBridged.lft macFas5.perChromTables = no macFas5.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} macFas5.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} macFas5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} macFas5.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} macFas5.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} macFas5.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} macFas5.downloadDir = macFas5 macFas5.refseq.mrna.native.load = yes macFas5.refseq.mrna.native.loadDesc = yes macFas5.refseq.mrna.xeno.load = yes macFas5.refseq.mrna.xeno.loadDesc = yes macFas5.genbank.mrna.native.load = yes macFas5.genbank.mrna.native.loadDesc = yes macFas5.genbank.est.native.load = yes macFas5.upstreamGeneTbl = refGene # rheMac10 Macaca mulatta (rhesus) (refseq assembly GCF_003339765.1) rheMac10.serverGenome = /hive/data/genomes/rheMac10/rheMac10.2bit rheMac10.ooc = /hive/data/genomes/rheMac10/jkStuff/rheMac10.11.ooc rheMac10.lift = /hive/data/genomes/rheMac10/jkStuff/rheMac10.nonBridged.lft rheMac10.perChromTables = no rheMac10.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} rheMac10.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} rheMac10.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} rheMac10.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} rheMac10.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} rheMac10.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} rheMac10.downloadDir = rheMac10 # DO NOT NEED genbank.mrna.xeno except for human, mouse(and in this case rhesus) rheMac10.refseq.mrna.native.load = yes rheMac10.refseq.mrna.xeno.load = yes rheMac10.upstreamGeneTbl = refGene # rheMac8 Macaca mulatta (rhesus) rheMac8.serverGenome = /hive/data/genomes/rheMac8/rheMac8.2bit rheMac8.ooc = /hive/data/genomes/rheMac8/jkStuff/rheMac8.11.ooc rheMac8.lift = /hive/data/genomes/rheMac8/jkStuff/nonBridged.lft rheMac8.perChromTables = no rheMac8.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} rheMac8.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} rheMac8.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} rheMac8.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} rheMac8.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} rheMac8.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} rheMac8.downloadDir = rheMac8 # DO NOT NEED genbank.mrna.xeno except for human, mouse(and in this case rhesus) rheMac8.refseq.mrna.native.load = yes rheMac8.refseq.mrna.xeno.load = yes rheMac8.upstreamGeneTbl = refGene # Rhesus macaque (macaca mulatta) rheMac2.serverGenome = /hive/data/genomes/rheMac2/rheMac2.2bit rheMac2.ooc = /hive/data/genomes/rheMac2/11.ooc rheMac2.lift = no rheMac2.downloadDir = rheMac2 rheMac2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} rheMac2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} rheMac2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} rheMac2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} rheMac2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse rheMac2.genbank.mrna.xeno.load = yes rheMac2.refseq.mrna.native.load = yes rheMac2.refseq.mrna.xeno.load = yes rheMac2.perChromTables = no rheMac2.upstreamGeneTbl = refGene # rheMac3 Rhesus macaque (macaca mulatta) rheMac3.serverGenome = /hive/data/genomes/rheMac3/rheMac3.2bit rheMac3.ooc = /hive/data/genomes/rheMac3/rheMac3.11.ooc rheMac3.lift = no rheMac3.perChromTables = no rheMac3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} rheMac3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} rheMac3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} rheMac3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} rheMac3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} rheMac3.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} rheMac3.downloadDir = rheMac3 # DO NOT NEED genbank.mrna.xeno except for human, mouse rheMac3.genbank.mrna.xeno.load = yes rheMac3.refseq.mrna.native.load = yes rheMac3.refseq.mrna.xeno.load = yes rheMac3.upstreamGeneTbl = refGene # chlSab2 (green monkey) (2,004 scaffolds N50 101219884) chlSab2.serverGenome = /hive/data/genomes/chlSab2/chlSab2.2bit chlSab2.ooc = /hive/data/genomes/chlSab2/jkStuff/chlSab2.11.ooc chlSab2.lift = /hive/data/genomes/chlSab2/jkStuff/chlSab2.nonBridged.lft chlSab2.perChromTables = no chlSab2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} chlSab2.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} chlSab2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} chlSab2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} chlSab2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} chlSab2.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} chlSab2.downloadDir = chlSab2 chlSab2.refseq.mrna.native.load = no chlSab2.refseq.mrna.xeno.load = yes chlSab2.refseq.mrna.xeno.loadDesc = yes chlSab2.genbank.mrna.native.load = yes chlSab2.genbank.mrna.native.loadDesc = no # DO NOT NEED genbank.mrna.xeno except for human, mouse chlSab2.genbank.mrna.xeno.load = no chlSab2.genbank.mrna.xeno.loadDesc = no chlSab2.genbank.est.native.load = yes chlSab2.genbank.est.native.loadDesc = yes # chlSab2.upstreamGeneTbl = ensGene # colAng1 (Colobus angolensis palliatus) (13,124 contigs, 86.6X coverage) colAng1.serverGenome = /hive/data/genomes/colAng1/colAng1.2bit colAng1.ooc = /hive/data/genomes/colAng1/jkStuff/colAng1.11.ooc colAng1.lift = no colAng1.perChromTables = no colAng1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} colAng1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} colAng1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} colAng1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} colAng1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} colAng1.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} colAng1.downloadDir = colAng1 # default yes refseq.mrna.native refseq.mrna.xeno genbank.mrna.native # default yes genbank.est.native # default no genbank.mrna.xeno genbank.est.xeno # colAng1.upstreamGeneTbl = ncbiGene # rhiBie1 - Rhinopithecus bieti - black snub-nosed monkey taxId 61621 rhiBie1.serverGenome = /hive/data/genomes/rhiBie1/rhiBie1.2bit rhiBie1.ooc = /hive/data/genomes/rhiBie1/jkStuff/rhiBie1.11.ooc rhiBie1.lift = no rhiBie1.perChromTables = no rhiBie1.downloadDir = rhiBie1 rhiBie1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} rhiBie1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} rhiBie1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} rhiBie1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} rhiBie1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults are fine: genbank.mrna.native refseq.mrna.native refseq.mrna.xeno yes # and genbank.est.native # rhiBie1.upstreamGeneTbl = refGene # rhiBie1.upstreamMaf = multiz7way # /hive/data/genomes/melGal4/bed/multiz7way/species.lst # rhiRox1 (Golden snub-nosed monkey) rhiRox1.serverGenome = /hive/data/genomes/rhiRox1/rhiRox1.2bit rhiRox1.ooc = /hive/data/genomes/rhiRox1/jkStuff/rhiRox1.11.ooc rhiRox1.lift = no rhiRox1.perChromTables = no rhiRox1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} rhiRox1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} rhiRox1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} rhiRox1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} rhiRox1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} rhiRox1.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} rhiRox1.downloadDir = rhiRox1 rhiRox1.refseq.mrna.native.load = no rhiRox1.refseq.mrna.native.loadDesc = no rhiRox1.refseq.mrna.xeno.load = yes rhiRox1.refseq.mrna.xeno.loadDesc = yes rhiRox1.genbank.mrna.native.load = no rhiRox1.genbank.mrna.native.loadDesc = no rhiRox1.genbank.est.native.load = no # rhiRox1.upstreamGeneTbl = refGene # nasLar1 (Proboscis monkey) nasLar1.serverGenome = /hive/data/genomes/nasLar1/nasLar1.2bit nasLar1.ooc = /hive/data/genomes/nasLar1/jkStuff/nasLar1.11.ooc nasLar1.lift = /hive/data/genomes/nasLar1/jkStuff/nasLar1.nonBridged.lft nasLar1.perChromTables = no nasLar1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} nasLar1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} nasLar1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} nasLar1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} nasLar1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} nasLar1.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} nasLar1.downloadDir = nasLar1 nasLar1.refseq.mrna.native.load = no nasLar1.refseq.mrna.native.loadDesc = no nasLar1.refseq.mrna.xeno.load = yes nasLar1.refseq.mrna.xeno.loadDesc = yes nasLar1.genbank.mrna.native.load = no nasLar1.genbank.mrna.native.loadDesc = no nasLar1.genbank.est.native.load = no nasLar1.upstreamGeneTbl = xenoRefGene # turTru2 (Dolphin) turTru2.serverGenome = /hive/data/genomes/turTru2/turTru2.2bit turTru2.ooc = /hive/data/genomes/turTru2/turTru2.11.ooc turTru2.lift = no turTru2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} turTru2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} turTru2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} turTru2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} turTru2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} turTru2.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} turTru2.refseq.mrna.native.load = no turTru2.refseq.mrna.xeno.load = yes turTru2.genbank.mrna.native.load = no turTru2.genbank.mrna.xeno.load = no turTru2.genbank.est.native.load = no turTru2.downloadDir = turTru2 turTru2.perChromTables = no # galGal2 (chicken) galGal2.serverGenome = /hive/data/genomes/galGal2/galGal2.2bit galGal2.ooc = /hive/data/genomes/galGal2/11.ooc galGal2.lift = /hive/data/genomes/galGal2/jkStuff/liftAll.lft galGal2.align.unplacedChroms = chrUn galGal2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} galGal2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} galGal2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} galGal2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} galGal2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} galGal2.refseq.mrna.native.load = yes galGal2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse galGal2.genbank.mrna.xeno.load = yes galGal2.downloadDir = galGal2 galGal2.upstreamGeneTbl = refGene galGal2.upstreamMaf = multiz7way /hive/data/genomes/galGal2/bed/multiz7way/species.lst # galGal3 galGal3.serverGenome = /hive/data/genomes/galGal3/galGal3.2bit galGal3.ooc = /hive/data/genomes/galGal3/11.ooc galGal3.align.unplacedChroms = chr*_random galGal3.lift = /hive/data/genomes/galGal3/jkStuff/liftAll.lft galGal3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} galGal3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} galGal3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} galGal3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} galGal3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} galGal3.refseq.mrna.native.load = yes galGal3.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse galGal3.genbank.mrna.xeno.load = yes galGal3.downloadDir = galGal3 galGal3.upstreamGeneTbl = refGene galGal3.upstreamMaf = multiz7way /hive/data/genomes/galGal3/bed/multiz7way/species.lst # galGal6 (chicken/GCF_000002315.5_GRCg6a) galGal6.serverGenome = /hive/data/genomes/galGal6/galGal6.2bit galGal6.ooc = /hive/data/genomes/galGal6/jkStuff/galGal6.11.ooc galGal6.lift = /hive/data/genomes/galGal6/jkStuff/nonBridged.lft galGal6.perChromTables = no galGal6.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} galGal6.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} galGal6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} galGal6.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} galGal6.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} galGal6.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} galGal6.refseq.mrna.native.load = yes galGal6.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse galGal6.genbank.mrna.xeno.load = yes galGal6.downloadDir = galGal6 # galGal6.upstreamGeneTbl = refGene # galGal6.upstreamMaf = multiz7way /hive/data/genomes/galGal4/bed/multiz7way/species.lst # galGal5 (chicken) galGal5.serverGenome = /hive/data/genomes/galGal5/galGal5.2bit galGal5.ooc = /hive/data/genomes/galGal5/jkStuff/galGal5.11.ooc galGal5.lift = /hive/data/genomes/galGal5/jkStuff/nonBridged.lft galGal5.perChromTables = no galGal5.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} galGal5.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} galGal5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} galGal5.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} galGal5.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} galGal5.refseq.mrna.native.load = yes galGal5.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse galGal5.genbank.mrna.xeno.load = yes galGal5.downloadDir = galGal5 # galGal5.upstreamGeneTbl = refGene # galGal5.upstreamMaf = multiz7way /hive/data/genomes/galGal4/bed/multiz7way/species.lst # galGal4 (chicken) galGal4.serverGenome = /hive/data/genomes/galGal4/galGal4.2bit galGal4.ooc = /hive/data/genomes/galGal4/jkStuff/galGal4.11.ooc galGal4.lift = /hive/data/genomes/galGal4/jkStuff/galGal4.nonBridged.lift galGal4.perChromTables = no galGal4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} galGal4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} galGal4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} galGal4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} galGal4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} galGal4.refseq.mrna.native.load = yes galGal4.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse galGal4.genbank.mrna.xeno.load = yes galGal4.downloadDir = galGal4 # galGal4.upstreamGeneTbl = refGene # galGal4.upstreamMaf = multiz7way /hive/data/genomes/galGal3/bed/multiz7way/species.lst # cotJap2 (Japanese quail/GCF_001577835.1_Coturnix_japonica_2.0) cotJap2.serverGenome = /hive/data/genomes/cotJap2/cotJap2.2bit cotJap2.ooc = /hive/data/genomes/cotJap2/jkStuff/cotJap2.11.ooc cotJap2.lift = /hive/data/genomes/cotJap2/jkStuff/nonBridged.lft cotJap2.perChromTables = no cotJap2.downloadDir = cotJap2 cotJap2.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} cotJap2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} cotJap2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} cotJap2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} cotJap2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} cotJap2.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc # cotJap2.upstreamGeneTbl = refGene # cotJap2.upstreamMaf = multiz7way /hive/data/genomes/galGal4/bed/multiz7way/species.lst # melGal5 (turkey) melGal5.serverGenome = /hive/data/genomes/melGal5/melGal5.2bit melGal5.ooc = /hive/data/genomes/melGal5/jkStuff/melGal5.11.ooc melGal5.lift = /hive/data/genomes/melGal5/jkStuff/nonBridged.lft melGal5.perChromTables = no melGal5.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} melGal5.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} melGal5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} melGal5.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} melGal5.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} melGal5.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} melGal5.downloadDir = melGal5 melGal5.refseq.mrna.native.load = yes melGal5.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse # melGal5.upstreamGeneTbl = ensGene # melGal1 (turkey) melGal1.serverGenome = /hive/data/genomes/melGal1/melGal1.2bit melGal1.ooc = /hive/data/genomes/melGal1/melGal1.11.ooc melGal1.lift = no melGal1.perChromTables = no melGal1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} melGal1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} melGal1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} melGal1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} melGal1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} melGal1.downloadDir = melGal1 melGal1.refseq.mrna.native.load = no melGal1.refseq.mrna.xeno.load = yes melGal1.refseq.mrna.xeno.loadDesc = yes melGal1.genbank.mrna.native.load = yes melGal1.genbank.mrna.native.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse melGal1.genbank.mrna.xeno.load = yes melGal1.genbank.mrna.xeno.loadDesc = yes melGal1.genbank.est.native.load = yes melGal1.genbank.est.native.loadDesc = yes melGal1.upstreamGeneTbl = ensGene # aquChr2 (golden eagle) aquChr2.serverGenome = /hive/data/genomes/aquChr2/aquChr2.2bit aquChr2.ooc = /hive/data/genomes/aquChr2/jkStuff/aquChr2.11.ooc aquChr2.lift = no aquChr2.perChromTables = no aquChr2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} aquChr2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} aquChr2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} aquChr2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} aquChr2.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} aquChr2.downloadDir = aquChr2 aquChr2.refseq.mrna.native.load = no aquChr2.refseq.mrna.xeno.load = yes aquChr2.refseq.mrna.xeno.loadDesc = yes aquChr2.genbank.mrna.native.load = no aquChr2.genbank.mrna.native.loadDesc = no # DO NOT NEED genbank.mrna.xeno except for human, mouse aquChr2.genbank.est.native.load = no aquChr2.genbank.est.native.loadDesc = no # aquChr2.upstreamGeneTbl = ensGene # myoLuc2 (Microbat) myoLuc2.serverGenome = /hive/data/genomes/myoLuc2/myoLuc2.2bit myoLuc2.ooc = /hive/data/genomes/myoLuc2/myoLuc2.11.ooc myoLuc2.lift = no myoLuc2.perChromTables = no myoLuc2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} myoLuc2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} myoLuc2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} myoLuc2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} myoLuc2.downloadDir = myoLuc2 myoLuc2.refseq.mrna.native.load = no myoLuc2.refseq.mrna.xeno.load = yes myoLuc2.refseq.mrna.xeno.loadDesc = yes myoLuc2.genbank.mrna.native.load = yes myoLuc2.genbank.mrna.native.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse myoLuc2.genbank.mrna.xeno.load = yes myoLuc2.genbank.mrna.xeno.loadDesc = yes myoLuc2.genbank.est.native.load = no myoLuc2.genbank.est.native.loadDesc = no myoLuc2.upstreamGeneTbl = ensGene # allMis1 - Alligator mississippiensis allMis1.serverGenome = /hive/data/genomes/allMis1/allMis1.2bit allMis1.ooc = /hive/data/genomes/allMis1/jkStuff/allMis1.11.ooc allMis1.lift = no allMis1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} allMis1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} allMis1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} allMis1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} allMis1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} allMis1.refseq.mrna.native.load = yes allMis1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse allMis1.genbank.mrna.xeno.load = yes allMis1.downloadDir = allMis1 allMis1.perChromTables = no # taeGut2 - Zebra Finch taeGut2.serverGenome = /hive/data/genomes/taeGut2/taeGut2.2bit taeGut2.ooc = /hive/data/genomes/taeGut2/jkStuff/taeGut2.11.ooc taeGut2.align.unplacedChroms = chrUn_*,chr*_random taeGut2.lift = /hive/data/genomes/taeGut2/jkStuff/taeGut2.nonBridged.lift taeGut2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} taeGut2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} taeGut2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} taeGut2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} taeGut2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} taeGut2.refseq.mrna.native.load = yes taeGut2.refseq.mrna.xeno.load = yes taeGut2.downloadDir = taeGut2 taeGut2.upstreamGeneTbl = refGene taeGut2.perChromTables = no # taeGut1 taeGut1.serverGenome = /hive/data/genomes/taeGut1/taeGut1.2bit taeGut1.ooc = /hive/data/genomes/taeGut1/taeGut1.11.ooc taeGut1.align.unplacedChroms = chrUn,chr*_random taeGut1.lift = /hive/data/genomes/taeGut1/jkStuff/liftAll.lft taeGut1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} taeGut1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} taeGut1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} taeGut1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} taeGut1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} taeGut1.refseq.mrna.native.load = yes taeGut1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse taeGut1.genbank.mrna.xeno.load = yes taeGut1.downloadDir = taeGut1 taeGut1.upstreamGeneTbl = refGene # ce11 (C. elegans) ce11.serverGenome = /hive/data/genomes/ce11/ce11.2bit ce11.ooc = /hive/data/genomes/ce11/jkStuff/ce11.11.ooc ce11.perChromTables = no ce11.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} ce11.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} ce11.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} ce11.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} ce11.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} ce11.maxIntron = 100000 ce11.lift = no ce11.refseq.mrna.native.load = yes ce11.refseq.mrna.xeno.load = yes ce11.genbank.mrna.xeno.load = yes ce11.genbank.mrna.native.load = yes ce11.genbank.est.native.load = yes ce11.downloadDir = ce11 # ce11.upstreamGeneTbl = ensGene # ce11.upstreamMaf = multiz7way /hive/data/genomes/ce11/bed/multiz7way/species.list # ce10 (C. elegans) ce10.serverGenome = /hive/data/genomes/ce10/ce10.2bit ce10.ooc = /hive/data/genomes/ce10/ce10.11.ooc ce10.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} ce10.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} ce10.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} ce10.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} ce10.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} ce10.maxIntron = 100000 ce10.lift = no # DO NOT NEED genbank.mrna.xeno except for human, mouse ce10.genbank.mrna.xeno.load = yes ce10.refseq.mrna.xeno.load = yes ce10.downloadDir = ce10 ce10.upstreamGeneTbl = ensGene ce10.upstreamMaf = multiz7way /hive/data/genomes/ce10/bed/multiz7way/species.list # ce6 (C. elegans) ce6.serverGenome = /hive/data/genomes/ce6/ce6.2bit ce6.ooc = /hive/data/genomes/ce6/11.ooc ce6.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} ce6.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} ce6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} ce6.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} ce6.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} ce6.maxIntron = 100000 ce6.lift = no # DO NOT NEED genbank.mrna.xeno except for human, mouse ce6.genbank.mrna.xeno.load = yes ce6.refseq.mrna.xeno.load = yes ce6.downloadDir = ce6 ce6.upstreamGeneTbl = ensGene ce6.upstreamMaf = multiz6way /hive/data/genomes/ce6/bed/multiz6way/species.lst # ce4 (C. elegans) ce4.serverGenome = /hive/data/genomes/ce4/ce4.2bit ce4.ooc = /hive/data/genomes/ce4/11.ooc ce4.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} ce4.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} ce4.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} ce4.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} ce4.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} ce4.maxIntron = 100000 ce4.lift = no # DO NOT NEED genbank.mrna.xeno except for human, mouse ce4.refseq.mrna.xeno.load = yes ce4.downloadDir = ce4 ce4.upstreamGeneTbl = refGene ce4.upstreamMaf = multiz5way /hive/data/genomes/ce4/bed/multiz5way/species.lst # ce2 (C. elegans) ce2.serverGenome = /hive/data/genomes/ce2/nib/chr*.nib ce2.ooc = /hive/data/genomes/ce2/11.ooc ce2.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} ce2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} ce2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} ce2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} ce2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} ce2.maxIntron = 100000 ce2.lift = no ce2.genbank.mrna.xeno.load = no ce2.downloadDir = ce2 ce2.upstreamGeneTbl = refGene # choHof1 (sloth) choHof1.serverGenome = /hive/data/genomes/choHof1/choHof1.2bit choHof1.ooc = /hive/data/genomes/choHof1//choHof1.11.ooc choHof1.lift = no choHof1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} choHof1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} choHof1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} choHof1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} choHof1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} choHof1.refseq.mrna.native.load = no choHof1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse choHof1.genbank.mrna.xeno.load = yes choHof1.genbank.est.native.load = no choHof1.downloadDir = choHof1 choHof1.perChromTables = no # chrPic2 (green painted turtle) chrPic2.serverGenome = /hive/data/genomes/chrPic2/chrPic2.2bit chrPic2.ooc = /hive/data/genomes/chrPic2/jkStuff/chrPic2.11.ooc chrPic2.lift = /hive/data/genomes/chrPic2/jkStuff/chrPic2.nonBridged.lift chrPic2.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} chrPic2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} chrPic2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} chrPic2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} chrPic2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} chrPic2.refseq.mrna.native.load = no chrPic2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse chrPic2.genbank.est.native.load = no chrPic2.downloadDir = chrPic2 chrPic2.perChromTables = no # chrPic1 (green painted turtle) chrPic1.serverGenome = /hive/data/genomes/chrPic1/chrPic1.2bit chrPic1.ooc = /hive/data/genomes/chrPic1/jkStuff/chrPic1.11.ooc chrPic1.lift = no chrPic1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} chrPic1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} chrPic1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} chrPic1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} chrPic1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} chrPic1.refseq.mrna.native.load = no chrPic1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse chrPic1.genbank.mrna.xeno.load = yes chrPic1.genbank.est.native.load = no chrPic1.downloadDir = chrPic1 chrPic1.perChromTables = no # dasNov3 (armadillo) dasNov3.serverGenome = /hive/data/genomes/dasNov3/dasNov3.2bit dasNov3.ooc = /hive/data/genomes/dasNov3/jkStuff/dasNov3.11.ooc dasNov3.lift = no dasNov3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} dasNov3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} dasNov3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} dasNov3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} dasNov3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} dasNov3.refseq.mrna.native.load = no dasNov3.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse dasNov3.genbank.mrna.xeno.load = yes dasNov3.genbank.est.native.load = no dasNov3.downloadDir = dasNov3 dasNov3.perChromTables = no # casCan1 (American beaver/Castor canadensis/taxId 51338) casCan1.serverGenome = /hive/data/genomes/casCan1/casCan1.2bit casCan1.ooc = /hive/data/genomes/casCan1/jkStuff/casCan1.11.ooc casCan1.lift = no casCan1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} casCan1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} casCan1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} casCan1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} casCan1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} casCan1.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc # yes: genbank.est.native.load refseq.mrna.native.load # yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load # yes: refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc # no: genbank.est.native.loadDesc genbank.est.xeno.load # no: genbank.est.xeno.loadDesc # there are zero native est or refSeq for casCan1 casCan1.genbank.est.native.load = no casCan1.refseq.mrna.native.load = no casCan1.refseq.mrna.native.loadDesc = no casCan1.downloadDir = casCan1 casCan1.perChromTables = no # dipOrd2 (Kangaroo rat) dipOrd2.serverGenome = /hive/data/genomes/dipOrd2/dipOrd2.2bit dipOrd2.ooc = /hive/data/genomes/dipOrd2/jkStuff/dipOrd2.11.ooc dipOrd2.lift = no dipOrd2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} dipOrd2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} dipOrd2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} dipOrd2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} dipOrd2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} # there are zero native mrna or est for dipOrd dipOrd2.refseq.mrna.native.load = no dipOrd2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse dipOrd2.genbank.mrna.xeno.load = yes dipOrd2.genbank.est.native.load = no dipOrd2.downloadDir = dipOrd2 dipOrd2.perChromTables = no # dipOrd1 (Kangaroo rat) dipOrd1.serverGenome = /hive/data/genomes/dipOrd1/dipOrd1.2bit dipOrd1.ooc = /hive/data/genomes/dipOrd1/dipOrd1.11.ooc dipOrd1.lift = no dipOrd1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} dipOrd1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} dipOrd1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} dipOrd1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} dipOrd1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} dipOrd1.refseq.mrna.native.load = no dipOrd1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse dipOrd1.genbank.mrna.xeno.load = yes dipOrd1.genbank.est.native.load = no dipOrd1.downloadDir = dipOrd1 dipOrd1.perChromTables = no # eriEur2 (European Hedgehog) eriEur2.serverGenome = /hive/data/genomes/eriEur2/eriEur2.2bit eriEur2.ooc = /hive/data/genomes/eriEur2/jkStuff/eriEur2.11.ooc eriEur2.lift = no eriEur2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} eriEur2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} eriEur2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} eriEur2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} eriEur2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} eriEur2.refseq.mrna.native.load = no eriEur2.refseq.mrna.xeno.load = yes eriEur2.genbank.mrna.xeno.load = no eriEur2.genbank.est.native.load = no eriEur2.downloadDir = eriEur2 eriEur2.perChromTables = no # eriEur1 (European Hedgehog) eriEur1.serverGenome = /hive/data/genomes/eriEur1/eriEur1.2bit eriEur1.ooc = /hive/data/genomes/eriEur1/eriEur1.11.ooc eriEur1.lift = no eriEur1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} eriEur1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} eriEur1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} eriEur1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} eriEur1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} eriEur1.refseq.mrna.native.load = no eriEur1.refseq.mrna.xeno.load = yes eriEur1.genbank.mrna.xeno.load = no eriEur1.genbank.est.native.load = no eriEur1.downloadDir = eriEur1 eriEur1.perChromTables = no # eulFla1 (Sclater's lemur / Eulemur flavifrons / taxId 87288) eulFla1.serverGenome = /hive/data/genomes/eulFla1/eulFla1.2bit eulFla1.ooc = /hive/data/genomes/eulFla1/jkStuff/eulFla1.11.ooc eulFla1.lift = no eulFla1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} eulFla1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} eulFla1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} eulFla1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} eulFla1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} eulFla1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} eulFla1.downloadDir = eulFla1 # there are no refseq mrna native eulFla1.refseq.mrna.native.load = no eulFla1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse eulFla1.genbank.mrna.xeno.load = no eulFla1.genbank.mrna.native.load = no eulFla1.genbank.est.native.load = no eulFla1.perChromTables = no # eulMac1 (Black lemur / Eulemur macaco / taxId 30602) eulMac1.serverGenome = /hive/data/genomes/eulMac1/eulMac1.2bit eulMac1.ooc = /hive/data/genomes/eulMac1/jkStuff/eulMac1.11.ooc eulMac1.lift = no eulMac1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} eulMac1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} eulMac1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} eulMac1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} eulMac1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} eulMac1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} eulMac1.downloadDir = eulMac1 # there are no refseq mrna native eulMac1.refseq.mrna.native.load = no eulMac1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse eulMac1.genbank.mrna.xeno.load = no eulMac1.genbank.mrna.native.load = no eulMac1.genbank.est.native.load = no eulMac1.perChromTables = no # gadMor1 (Atlantic cod) gadMor1.serverGenome = /hive/data/genomes/gadMor1/gadMor1.2bit gadMor1.ooc = /hive/data/genomes/gadMor1/jkStuff/gadMor1.11.ooc gadMor1.lift = no gadMor1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} gadMor1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} gadMor1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} gadMor1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} gadMor1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} gadMor1.refseq.mrna.native.load = no gadMor1.refseq.mrna.xeno.load = yes gadMor1.genbank.mrna.xeno.load = no gadMor1.genbank.est.native.load = yes gadMor1.downloadDir = gadMor1 gadMor1.perChromTables = no # aptMan1 (brown kiwi) aptMan1.serverGenome = /hive/data/genomes/aptMan1/aptMan1.2bit aptMan1.ooc = /hive/data/genomes/aptMan1/jkStuff/aptMan1.11.ooc aptMan1.lift = no aptMan1.perChromTables = no aptMan1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} aptMan1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} aptMan1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} aptMan1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} aptMan1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} aptMan1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} aptMan1.downloadDir = aptMan1 # defaults are OK: genbank and refseq mrna.native.load yes # genbank est.native.load yes refseq.mrna.xeno.load yes # genbank mrna and est xeno.load no # ficAlb1 (Ficedula albicollis - collard flycatcher) - taxId: 59894 ficAlb1.serverGenome = /hive/data/genomes/ficAlb1/ficAlb1.2bit ficAlb1.ooc = /hive/data/genomes/ficAlb1/jkStuff/ficAlb1.11.ooc ficAlb1.lift = /hive/data/genomes/ficAlb1/jkStuff/nonBridged.lft ficAlb1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} ficAlb1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} ficAlb1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} ficAlb1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} ficAlb1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # defaults yes: genbank.mrna.native.load and loadDesc # defaults yes: genbank.est.native.load # defaults yes: refseq.mrna.native.load, refseq.mrna.native.loadDesc # defaults yes: refseq.mrna.xeno.load, refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load and loadDesc # defaults no: genbank.est.xeno.load, genbank.est.xeno.loadDesc # DO NOT NEED genbank.mrna.xeno except for human, mouse # there are no genbank.est natives: ficAlb1.genbank.est.native.load = no ficAlb1.downloadDir = ficAlb1 ficAlb1.perChromTables = no # geoFor1 (Medium Ground Finch - Darwin finch) geoFor1.serverGenome = /hive/data/genomes/geoFor1/geoFor1.2bit geoFor1.ooc = /hive/data/genomes/geoFor1/jkStuff/geoFor1.11.ooc geoFor1.lift = no geoFor1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} geoFor1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} geoFor1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} geoFor1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} geoFor1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} geoFor1.refseq.mrna.native.load = no geoFor1.refseq.mrna.xeno.load = yes geoFor1.genbank.mrna.xeno.load = no geoFor1.genbank.est.native.load = no geoFor1.downloadDir = geoFor1 geoFor1.perChromTables = no geoFor1.upstreamGeneTbl = xenoRefGene geoFor1.upstreamMaf = multiz7way /hive/data/genomes/geoFor1/bed/multiz7way/species.list # latCha1 (Coelacanth) latCha1.serverGenome = /hive/data/genomes/latCha1/latCha1.2bit latCha1.ooc = /hive/data/genomes/latCha1/jkStuff/latCha1.11.ooc latCha1.lift = no latCha1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} latCha1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} latCha1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} latCha1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} latCha1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} latCha1.refseq.mrna.native.load = no latCha1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse latCha1.genbank.mrna.xeno.load = yes latCha1.genbank.est.native.load = no latCha1.downloadDir = latCha1 latCha1.perChromTables = no # manPen1 (Pangolin) 92770 contigs manPen1.serverGenome = /hive/data/genomes/manPen1/manPen1.2bit manPen1.ooc = /hive/data/genomes/manPen1/jkStuff/manPen1.11.ooc manPen1.lift = no manPen1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} manPen1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} manPen1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} manPen1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} manPen1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} manPen1.refseq.mrna.native.load = no manPen1.refseq.mrna.xeno.load = yes manPen1.genbank.mrna.xeno.load = no manPen1.genbank.mrna.native.load = no manPen1.genbank.est.native.load = no manPen1.downloadDir = manPen1 manPen1.perChromTables = no # melUnd1 (Budgerigar) melUnd1.serverGenome = /hive/data/genomes/melUnd1/melUnd1.2bit melUnd1.ooc = /hive/data/genomes/melUnd1/jkStuff/melUnd1.11.ooc melUnd1.lift = no melUnd1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} melUnd1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} melUnd1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} melUnd1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} melUnd1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} melUnd1.refseq.mrna.native.load = no melUnd1.refseq.mrna.xeno.load = yes melUnd1.genbank.mrna.xeno.load = no melUnd1.genbank.est.native.load = no melUnd1.downloadDir = melUnd1 melUnd1.perChromTables = no # galVar1 - Galeopterus variegatus - Malayan flying lemur galVar1.serverGenome = /hive/data/genomes/galVar1/galVar1.2bit galVar1.ooc = /hive/data/genomes/galVar1/jkStuff/galVar1.11.ooc galVar1.lift = no galVar1.perChromTables = no galVar1.downloadDir = galVar1 galVar1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} galVar1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} galVar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} galVar1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} galVar1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} galVar1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # the defaults: genbank.mrna.native.load, yes genbank.est.native.load yes # refseq.mrna.native.load yes, refseq.mrna.xeno.load yes # are good enough even though nothing exists for 'native' for this one # galVar1.upstreamGeneTbl = refGene # micMur3 (Mouse lemur) micMur3.serverGenome = /hive/data/genomes/micMur3/micMur3.2bit micMur3.ooc = /hive/data/genomes/micMur3/jkStuff/micMur3.11.ooc micMur3.lift = no micMur3.perChromTables = no micMur3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} micMur3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} micMur3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} micMur3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} micMur3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} micMur3.refseq.mrna.native.load = no micMur3.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse # the defaults: genbank.mrna.native.load, yes genbank.est.native.load yes # refseq.mrna.native.load yes, refseq.mrna.xeno.load yes # there are no native est micMur3.genbank.est.native.load = no micMur3.downloadDir = micMur3 # micMur2 (Mouse lemur) micMur2.serverGenome = /hive/data/genomes/micMur2/micMur2.2bit micMur2.ooc = /hive/data/genomes/micMur2/jkStuff/micMur2.11.ooc micMur2.lift = no micMur2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} micMur2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} micMur2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} micMur2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} micMur2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} micMur2.refseq.mrna.native.load = no micMur2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse micMur2.genbank.mrna.xeno.load = no micMur2.genbank.est.native.load = no micMur2.downloadDir = micMur2 micMur2.perChromTables = no # micMur1 (Mouse lemur) micMur1.serverGenome = /hive/data/genomes/micMur1/micMur1.2bit micMur1.ooc = /hive/data/genomes/micMur1/jkStuff/micMur1.11.ooc micMur1.lift = no micMur1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} micMur1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} micMur1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} micMur1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} micMur1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} micMur1.refseq.mrna.native.load = no micMur1.refseq.mrna.xeno.load = yes micMur1.genbank.mrna.xeno.load = no micMur1.genbank.est.native.load = no micMur1.downloadDir = micMur1 micMur1.perChromTables = no # ochPri3 (Pika) ochPri3.serverGenome = /hive/data/genomes/ochPri3/ochPri3.2bit ochPri3.ooc = /hive/data/genomes/ochPri3/jkStuff/ochPri3.11.ooc ochPri3.lift = no ochPri3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} ochPri3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} ochPri3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} ochPri3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} ochPri3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} ochPri3.refseq.mrna.native.load = no ochPri3.refseq.mrna.xeno.load = yes ochPri3.genbank.mrna.xeno.load = no ochPri3.genbank.est.native.load = no ochPri3.downloadDir = ochPri3 ochPri3.perChromTables = no # ochPri2 (Pika) ochPri2.serverGenome = /hive/data/genomes/ochPri2/ochPri2.2bit ochPri2.ooc = /hive/data/genomes/ochPri2/jkStuff/ochPri2.11.ooc ochPri2.lift = no ochPri2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ochPri2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ochPri2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ochPri2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ochPri2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} ochPri2.refseq.mrna.native.load = no ochPri2.refseq.mrna.xeno.load = yes ochPri2.genbank.mrna.xeno.load = no ochPri2.genbank.est.native.load = no ochPri2.downloadDir = ochPri2 ochPri2.perChromTables = no # oreNil3 (Nile tilapia) oreNil3.serverGenome = /hive/data/genomes/oreNil3/oreNil3.2bit oreNil3.ooc = /hive/data/genomes/oreNil3/jkStuff/oreNil3.11.ooc oreNil3.lift = no oreNil3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} oreNil3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} oreNil3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} oreNil3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} oreNil3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} oreNil3.refseq.mrna.native.load = yes oreNil3.refseq.mrna.xeno.load = yes oreNil3.genbank.mrna.xeno.load = no oreNil3.genbank.est.native.load = yes oreNil3.downloadDir = oreNil3 oreNil3.perChromTables = no # oreNil2 (Nile tilapia) oreNil2.serverGenome = /hive/data/genomes/oreNil2/oreNil2.2bit oreNil2.ooc = /hive/data/genomes/oreNil2/jkStuff/oreNil2.11.ooc oreNil2.lift = /hive/data/genomes/oreNil2/jkStuff/oreNil2.nonBridged.lift oreNil2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} oreNil2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} oreNil2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} oreNil2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} oreNil2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} oreNil2.refseq.mrna.native.load = yes oreNil2.refseq.mrna.xeno.load = yes oreNil2.genbank.mrna.xeno.load = no oreNil2.genbank.est.native.load = yes oreNil2.downloadDir = oreNil2 oreNil2.perChromTables = no # ascSuu1 (Pig roundworm/Ascaris suum) ascSuu1.serverGenome = /hive/data/genomes/ascSuu1/ascSuu1.2bit ascSuu1.ooc = /hive/data/genomes/ascSuu1/jkStuff/ascSuu1.11.ooc ascSuu1.lift = no # the nematodes have small introns ascSuu1.maxIntron = 100000 ascSuu1.perChromTables = no ascSuu1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ascSuu1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ascSuu1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ascSuu1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ascSuu1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} # refseq.mrna native and xeno are default yes # genbank.mrna and genbank.est native are default yes, the xeno is default no ascSuu1.downloadDir = ascSuu1 # priExs1 (P. exspectatus/Pristionchus exspectatus) priExs1.serverGenome = /hive/data/genomes/priExs1/priExs1.2bit priExs1.ooc = /hive/data/genomes/priExs1/jkStuff/priExs1.11.ooc priExs1.lift = /hive/data/genomes/priExs1/jkStuff/priExs1.nonBridged.lft # the nematodes have small introns priExs1.maxIntron = 100000 priExs1.perChromTables = no priExs1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} priExs1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} priExs1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} priExs1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} priExs1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} # refseq.mrna native and xeno are default yes # genbank.mrna and genbank.est native are default yes, the xeno is default no priExs1.downloadDir = priExs1 # ancCey1 (A. ceylanicum) ancCey1.serverGenome = /hive/data/genomes/ancCey1/ancCey1.2bit ancCey1.ooc = /hive/data/genomes/ancCey1/jkStuff/ancCey1.11.ooc ancCey1.lift = no # the nematodes have small introns ancCey1.maxIntron = 10 ancCey1.perChromTables = no ancCey1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ancCey1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ancCey1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ancCey1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ancCey1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} # refseq.mrna native and xeno are default yes # genbank.mrna and genbank.est native are default yes, the xeno is default no ancCey1.downloadDir = ancCey1 # priPac3 (P. pacificus) priPac3.serverGenome = /hive/data/genomes/priPac3/priPac3.2bit priPac3.ooc = /hive/data/genomes/priPac3/jkStuff/priPac3.11.ooc priPac3.lift = /hive/data/genomes/priPac3/jkStuff/priPac3.nonBridged.lft priPac3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} priPac3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} priPac3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} priPac3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} priPac3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} priPac3.refseq.mrna.native.load = yes priPac3.refseq.mrna.xeno.load = yes priPac3.refseq.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse priPac3.genbank.mrna.xeno.load = no priPac3.genbank.est.native.load = yes priPac3.genbank.est.native.loadDesc = no priPac3.downloadDir = priPac3 priPac3.perChromTables = no # priPac1 (P. pacificus) priPac1.serverGenome = /hive/data/genomes/priPac1/priPac1.2bit priPac1.ooc = /hive/data/genomes/priPac1/11.ooc priPac1.lift = /hive/data/genomes/priPac1/jkStuff/priPac1.supercontigs.lift priPac1.align.unplacedChroms = chrUn priPac1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} priPac1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} priPac1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} priPac1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} priPac1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} priPac1.refseq.mrna.native.load = no priPac1.refseq.mrna.xeno.load = yes priPac1.refseq.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse priPac1.genbank.est.native.load = yes priPac1.genbank.est.native.loadDesc = no priPac1.downloadDir = priPac1 priPac1.perChromTables = no # proCap1 (Rock hyrax) proCap1.serverGenome = /hive/data/genomes/proCap1/proCap1.2bit proCap1.ooc = /hive/data/genomes/proCap1/jkStuff/proCap1.11.ooc proCap1.lift = no proCap1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} proCap1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} proCap1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} proCap1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} proCap1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} proCap1.refseq.mrna.native.load = no proCap1.refseq.mrna.xeno.load = yes proCap1.genbank.mrna.xeno.load = no proCap1.genbank.est.native.load = no proCap1.downloadDir = proCap1 proCap1.perChromTables = no # pteVam1 (megabat) pteVam1.serverGenome = /hive/data/genomes/pteVam1/pteVam1.2bit pteVam1.ooc = /hive/data/genomes/pteVam1/jkStuff/pteVam1.11.ooc pteVam1.lift = no pteVam1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} pteVam1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} pteVam1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} pteVam1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} pteVam1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} pteVam1.refseq.mrna.native.load = no pteVam1.refseq.mrna.xeno.load = yes pteVam1.genbank.mrna.xeno.load = no pteVam1.genbank.est.native.load = no pteVam1.downloadDir = pteVam1 pteVam1.perChromTables = no # rouAeg1 Rousettus aegyptiacus (Egyptian rousette (fruit bat)) rouAeg1.serverGenome = /hive/data/genomes/rouAeg1/rouAeg1.2bit rouAeg1.ooc = /hive/data/genomes/rouAeg1/jkStuff/rouAeg1.11.ooc rouAeg1.lift = no rouAeg1.perChromTables = no rouAeg1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} rouAeg1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} rouAeg1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} rouAeg1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} rouAeg1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} rouAeg1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} # refseq.mrna native and xeno are default yes # genbank.mrna and genbank.est native are default yes, the xeno is default no rouAeg1.refseq.mrna.native.load = no rouAeg1.genbank.est.native.load = no rouAeg1.downloadDir = rouAeg1 # saiBol1 (squirrel monkey) saiBol1.serverGenome = /hive/data/genomes/saiBol1/saiBol1.2bit saiBol1.ooc = /hive/data/genomes/saiBol1/jkStuff/saiBol1.11.ooc saiBol1.lift = no saiBol1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} saiBol1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} saiBol1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} saiBol1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} saiBol1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} saiBol1.refseq.mrna.native.load = no saiBol1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse saiBol1.genbank.mrna.xeno.load = yes saiBol1.genbank.est.native.load = no saiBol1.downloadDir = saiBol1 saiBol1.perChromTables = no # sorAra2 (common shrew) sorAra2.serverGenome = /hive/data/genomes/sorAra2/sorAra2.2bit sorAra2.ooc = /hive/data/genomes/sorAra2/jkStuff/sorAra2.11.ooc sorAra2.lift = no sorAra2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} sorAra2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} sorAra2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} sorAra2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} sorAra2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} sorAra2.refseq.mrna.native.load = no sorAra2.refseq.mrna.xeno.load = yes sorAra2.genbank.mrna.xeno.load = no sorAra2.genbank.est.native.load = no sorAra2.downloadDir = sorAra2 sorAra2.perChromTables = no # sorAra1 (common shrew) sorAra1.serverGenome = /hive/data/genomes/sorAra1/sorAra1.2bit sorAra1.ooc = /hive/data/genomes/sorAra1/jkStuff/sorAra1.11.ooc sorAra1.lift = no sorAra1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} sorAra1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} sorAra1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} sorAra1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} sorAra1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} sorAra1.refseq.mrna.native.load = no sorAra1.refseq.mrna.xeno.load = yes sorAra1.genbank.mrna.xeno.load = no sorAra1.genbank.est.native.load = no sorAra1.downloadDir = sorAra1 sorAra1.perChromTables = no # speTri2 (13-lined ground squirrel) speTri2.serverGenome = /hive/data/genomes/speTri2/speTri2.2bit speTri2.ooc = /hive/data/genomes/speTri2/jkStuff/speTri2.11.ooc speTri2.lift = no speTri2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} speTri2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} speTri2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} speTri2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} speTri2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} speTri2.refseq.mrna.native.load = no speTri2.refseq.mrna.xeno.load = yes speTri2.genbank.mrna.xeno.load = no speTri2.genbank.est.native.load = yes speTri2.downloadDir = speTri2 speTri2.perChromTables = no # tarSyr2 (Tarsier) tarSyr2.serverGenome = /hive/data/genomes/tarSyr2/tarSyr2.2bit tarSyr2.ooc = /hive/data/genomes/tarSyr2/jkStuff/tarSyr2.11.ooc tarSyr2.lift = no tarSyr2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} tarSyr2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} tarSyr2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} tarSyr2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} tarSyr2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} tarSyr2.refseq.mrna.native.load = no tarSyr2.refseq.mrna.xeno.load = yes tarSyr2.genbank.mrna.xeno.load = no tarSyr2.genbank.est.native.load = no tarSyr2.downloadDir = tarSyr2 tarSyr2.perChromTables = no # tarSyr1 (Tarsier) tarSyr1.serverGenome = /hive/data/genomes/tarSyr1/tarSyr1.2bit tarSyr1.ooc = /hive/data/genomes/tarSyr1/tarSyr1.11.ooc tarSyr1.lift = no tarSyr1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} tarSyr1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} tarSyr1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} tarSyr1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} tarSyr1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} tarSyr1.refseq.mrna.native.load = no tarSyr1.refseq.mrna.xeno.load = yes tarSyr1.genbank.mrna.xeno.load = no tarSyr1.genbank.est.native.load = yes tarSyr1.downloadDir = tarSyr1 tarSyr1.perChromTables = no # tupChi1 (Chinese shrew) tupChi1.serverGenome = /hive/data/genomes/tupChi1/tupChi1.2bit tupChi1.ooc = /hive/data/genomes/tupChi1/jkStuff/tupChi1.11.ooc tupChi1.lift = no tupChi1.perChromTables = no tupChi1.downloadDir = tupChi1 tupChi1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} tupChi1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} tupChi1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} tupChi1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} tupChi1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # the defaults: genbank.mrna.native.load, yes genbank.est.native.load yes # refseq.mrna.native.load yes, refseq.mrna.xeno.load yes # tupBel1 (common shrew) tupBel1.serverGenome = /hive/data/genomes/tupBel1/tupBel1.2bit tupBel1.ooc = /hive/data/genomes/tupBel1/tupBel1.11.ooc tupBel1.lift = /hive/data/genomes/tupBel1/jkStuff/tupBel1.nonBridged.lift tupBel1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} tupBel1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} tupBel1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} tupBel1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} tupBel1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} tupBel1.refseq.mrna.native.load = no tupBel1.refseq.mrna.xeno.load = yes tupBel1.genbank.mrna.xeno.load = no tupBel1.genbank.est.native.load = yes tupBel1.downloadDir = tupBel1 tupBel1.perChromTables = no # vicPac2 (alpaca) vicPac2.serverGenome = /hive/data/genomes/vicPac2/vicPac2.2bit vicPac2.ooc = /hive/data/genomes/vicPac2/jkStuff/vicPac2.11.ooc vicPac2.lift = no vicPac2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} vicPac2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} vicPac2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} vicPac2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} vicPac2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} vicPac2.downloadDir = vicPac2 vicPac2.perChromTables = no # vicPac1 (alpaca) vicPac1.serverGenome = /hive/data/genomes/vicPac1/vicPac1.2bit vicPac1.ooc = /hive/data/genomes/vicPac1/jkStuff/vicPac1.11.ooc vicPac1.lift = no vicPac1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} vicPac1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} vicPac1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} vicPac1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} vicPac1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} vicPac1.refseq.mrna.native.load = no vicPac1.refseq.mrna.xeno.load = yes vicPac1.genbank.mrna.native.load = no vicPac1.genbank.mrna.xeno.load = no vicPac1.genbank.est.native.load = yes vicPac1.downloadDir = vicPac1 vicPac1.perChromTables = no # balAcu1 (minke whale) balAcu1.serverGenome = /hive/data/genomes/balAcu1/balAcu1.2bit balAcu1.ooc = /hive/data/genomes/balAcu1/jkStuff/balAcu1.11.ooc balAcu1.lift = no balAcu1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} balAcu1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} balAcu1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} balAcu1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} balAcu1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} balAcu1.refseq.mrna.native.load = no balAcu1.refseq.mrna.xeno.load = yes balAcu1.genbank.mrna.xeno.load = no balAcu1.genbank.est.native.load = no balAcu1.genbank.mrna.native.load = no balAcu1.genbank.mrna.native.loadDesc = no balAcu1.downloadDir = balAcu1 balAcu1.perChromTables = no # orcOrc1 (killer whale) orcOrc1.serverGenome = /hive/data/genomes/orcOrc1/orcOrc1.2bit orcOrc1.ooc = /hive/data/genomes/orcOrc1/jkStuff/orcOrc1.11.ooc orcOrc1.lift = no orcOrc1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} orcOrc1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} orcOrc1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} orcOrc1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} orcOrc1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} orcOrc1.refseq.mrna.native.load = no orcOrc1.refseq.mrna.xeno.load = yes orcOrc1.genbank.mrna.xeno.load = no orcOrc1.genbank.est.native.load = no orcOrc1.genbank.mrna.native.load = no orcOrc1.genbank.mrna.native.loadDesc = no orcOrc1.downloadDir = orcOrc1 orcOrc1.perChromTables = no # refseq.mrna native and xeno are default yes # genbank.mrna and genbank.est native are default yes, the xeno is default no orcOrc1.genbank.est.native.load = no # calMil1 (Elephant shark) calMil1.serverGenome = /hive/data/genomes/calMil1/calMil1.2bit calMil1.ooc = /hive/data/genomes/calMil1/jkStuff/calMil1.11.ooc calMil1.lift = no calMil1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} calMil1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} calMil1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} calMil1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} calMil1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} calMil1.refseq.mrna.native.load = no calMil1.refseq.mrna.xeno.load = yes calMil1.genbank.mrna.xeno.load = no calMil1.genbank.est.native.load = yes calMil1.genbank.mrna.native.load = yes calMil1.genbank.mrna.native.loadDesc = no calMil1.downloadDir = calMil1 calMil1.perChromTables = no # caePb2 (C. brenneri) caePb2.serverGenome = /hive/data/genomes/caePb2/caePb2.2bit caePb2.ooc = /hive/data/genomes/caePb2/11.ooc caePb2.lift = /hive/data/genomes/caePb2/jkStuff/caePb2.supercontigs.lift caePb2.align.unplacedChroms = chrUn caePb2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} caePb2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} caePb2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} caePb2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} caePb2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} caePb2.refseq.mrna.native.load = no caePb2.refseq.mrna.xeno.load = yes caePb2.refseq.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse caePb2.genbank.mrna.xeno.load = yes caePb2.genbank.est.native.load = yes caePb2.genbank.est.native.loadDesc = no caePb2.downloadDir = caePb2 caePb2.perChromTables = no # caePb1 (C. brenneri aka C. PB2801) caePb1.serverGenome = /hive/data/genomes/caePb1/caePb1.2bit caePb1.ooc = /hive/data/genomes/caePb1/11.ooc caePb1.lift = /hive/data/genomes/caePb1/jkStuff/caePb1.supercontigs.lift caePb1.align.unplacedChroms = chrUn caePb1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} caePb1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} caePb1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} caePb1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} caePb1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} caePb1.refseq.mrna.native.load = no caePb1.refseq.mrna.xeno.load = yes caePb1.refseq.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse caePb1.genbank.est.native.load = no caePb1.genbank.est.native.loadDesc = no caePb1.downloadDir = caePb1 caePb1.perChromTables = no # caeRem3 (C. remanei) caeRem3.serverGenome = /hive/data/genomes/caeRem3/caeRem3.2bit caeRem3.ooc = /hive/data/genomes/caeRem3/11.ooc caeRem3.lift = /hive/data/genomes/caeRem3/downloads/caeRem3.chrUn.lift caeRem3.align.unplacedChroms = chrUn caeRem3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} caeRem3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} caeRem3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} caeRem3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} caeRem3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} caeRem3.refseq.mrna.native.load = no caeRem3.refseq.mrna.xeno.load = yes caeRem3.refseq.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse caeRem3.genbank.mrna.xeno.load = yes caeRem3.genbank.est.native.load = yes caeRem3.genbank.est.native.loadDesc = no caeRem3.downloadDir = caeRem3 caeRem3.perChromTables = no # caeRem2 (C. remanei) caeRem2.serverGenome = /hive/data/genomes/caeRem2/caeRem2.2bit caeRem2.ooc = /hive/data/genomes/caeRem2/11.ooc caeRem2.lift = /hive/data/genomes/caeRem2/jkStuff/caeRem2.chrUn.lift caeRem2.align.unplacedChroms = chrUn caeRem2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} caeRem2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} caeRem2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} caeRem2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} caeRem2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} caeRem2.refseq.mrna.native.load = no caeRem2.refseq.mrna.xeno.load = yes caeRem2.refseq.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse caeRem2.genbank.est.native.load = yes caeRem2.genbank.est.native.loadDesc = no caeRem2.downloadDir = caeRem2 caeRem2.perChromTables = no # caeJap1 (C. japonica) caeJap1.serverGenome = /hive/data/genomes/caeJap1/caeJap1.2bit caeJap1.ooc = /hive/data/genomes/caeJap1/11.ooc caeJap1.lift = /hive/data/genomes/caeJap1/jkStuff/caeJap1.chrUn.lift caeJap1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} caeJap1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} caeJap1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} caeJap1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} caeJap1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} caeJap1.refseq.mrna.native.load = yes caeJap1.refseq.mrna.xeno.load = yes caeJap1.refseq.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse caeJap1.genbank.mrna.xeno.load = yes caeJap1.genbank.est.native.load = yes caeJap1.genbank.est.native.loadDesc = no caeJap1.downloadDir = caeJap1 caeJap1.perChromTables = no # Marmoset calJac3.serverGenome = /hive/data/genomes/calJac3/calJac3.2bit calJac3.ooc = /hive/data/genomes/calJac3/calJac3.11.ooc calJac3.lift = no calJac3.perChromTables = no calJac3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} calJac3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} calJac3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} calJac3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} calJac3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} calJac3.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} calJac3.downloadDir = calJac3 calJac3.refseq.mrna.native.load = yes calJac3.refseq.mrna.xeno.load = yes calJac3.refseq.mrna.xeno.loadDesc = yes calJac3.genbank.mrna.xeno.load = yes calJac3.upstreamGeneTbl = ensGene calJac3.upstreamMaf = multiz13way /hive/data/genomes/calJac3/bed/multiz13way/species.list # Marmoset calJac1.serverGenome = /hive/data/genomes/calJac1/calJac1.2bit calJac1.ooc = /hive/data/genomes/calJac1/11.ooc calJac1.lift = no calJac1.perChromTables = no calJac1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} calJac1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} calJac1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} calJac1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} calJac1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} calJac1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} calJac1.downloadDir = calJac1 calJac1.refseq.mrna.native.load = yes calJac1.refseq.mrna.xeno.load = yes calJac1.refseq.mrna.xeno.loadDesc = yes calJac1.upstreamGeneTbl = xenoRefGene calJac1.upstreamMaf = multiz9way /hive/data/genomes/calJac1/bed/multiz9way/species.list # danRer3 (zebrafish) # Lift file partitions unplaced sequence pseudo-chroms danRer3.serverGenome = /hive/data/genomes/danRer3/danRer3.2bit danRer3.ooc = /hive/data/genomes/danRer3/danRer3_11.ooc danRer3.align.unplacedChroms = chrNA,chrUn danRer3.lift = /hive/data/genomes/danRer3/liftSupertoChrom/liftNAandUnScaffoldsToChrom.lft danRer3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} danRer3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} danRer3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} danRer3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} danRer3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} danRer3.downloadDir = danRer3 danRer3.mgc = yes danRer3.upstreamGeneTbl = refGene danRer3.upstreamMaf = multiz5way /hive/data/genomes/danRer3/bed/multiz5way/species.list # danRer4 (zebrafish) # Lift file partitions unplaced sequence pseudo-chroms danRer4.serverGenome = /hive/data/genomes/danRer4/danRer4.2bit danRer4.ooc = /hive/data/genomes/danRer4/danRer4_11.ooc danRer4.lift = /hive/data/genomes/danRer4/jkStuff/liftAll.lft danRer4.align.unplacedChroms = chrNA_random,chrUn_random danRer4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} danRer4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} danRer4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} danRer4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} danRer4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} danRer4.downloadDir = danRer4 danRer4.mgc = yes danRer4.upstreamGeneTbl = refGene danRer4.upstreamMaf = multiz7way /hive/data/genomes/danRer4/bed/multiz7way/species.lst # danRer5 (zebrafish) danRer5.serverGenome = /hive/data/genomes/danRer5/danRer5.2bit danRer5.ooc = /hive/data/genomes/danRer5/danRer5_11.ooc danRer5.lift = /hive/data/genomes/danRer5/jkStuff/nonBridgedGap.lft danRer5.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} danRer5.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} danRer5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} danRer5.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} danRer5.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} danRer5.downloadDir = danRer5 danRer5.perChromTables = no danRer5.mgc = yes danRer5.orfeome = yes danRer5.upstreamGeneTbl = refGene # danRer6 (zebrafish) danRer6.serverGenome = /hive/data/genomes/danRer6/danRer6.2bit danRer6.ooc = /hive/data/genomes/danRer6/11.ooc danRer6.lift = /hive/data/genomes/danRer6/jkStuff/danRer6.unBridged.lift danRer6.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} danRer6.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} danRer6.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} danRer6.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} danRer6.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} danRer6.genbank.mrna.xeno.load = yes danRer6.downloadDir = danRer6 danRer6.perChromTables = no danRer6.refseq.mrna.xeno.load = yes danRer6.mgc = yes danRer6.orfeome = yes danRer6.upstreamGeneTbl = refGene danRer6.upstreamMaf = multiz6way /hive/data/genomes/danRer6/bed/multiz6way/species.lst # danRer7 (zebrafish) danRer7.serverGenome = /hive/data/genomes/danRer7/danRer7.2bit danRer7.ooc = /hive/data/genomes/danRer7/danRer7.11.ooc danRer7.lift = no danRer7.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} danRer7.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} danRer7.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} danRer7.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} danRer7.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} danRer7.genbank.mrna.xeno.load = yes danRer7.downloadDir = danRer7 danRer7.perChromTables = no danRer7.refseq.mrna.xeno.load = yes danRer7.mgc = yes danRer7.orfeome = yes danRer7.upstreamGeneTbl = ensGene danRer7.upstreamMaf = multiz8way /hive/data/genomes/danRer7/bed/multiz8way/species.lst # danRer10 (zebrafish) danRer10.serverGenome = /hive/data/genomes/danRer10/danRer10.2bit danRer10.ooc = /hive/data/genomes/danRer10/jkStuff/danRer10.11.ooc danRer10.lift = no danRer10.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} danRer10.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} danRer10.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} danRer10.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} danRer10.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} danRer10.genbank.mrna.xeno.load = yes danRer10.downloadDir = danRer10 danRer10.perChromTables = no danRer10.refseq.mrna.xeno.load = yes danRer10.mgc = yes danRer10.orfeome = yes # danRer10.upstreamGeneTbl = ensGene # danRer10.upstreamMaf = multiz8way /hive/data/genomes/danRer10/bed/multiz8way/species.lst # danRer11 (zebrafish) danRer11.serverGenome = /hive/data/genomes/danRer11/danRer11.2bit danRer11.ooc = /hive/data/genomes/danRer11/jkStuff/danRer11.11.ooc danRer11.lift = /hive/data/genomes/danRer11/jkStuff/nonBridged.lft danRer11.perChromTables = no danRer11.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} danRer11.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} danRer11.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} danRer11.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} danRer11.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults are fine: genbank.mrna.native refseq.mrna.native refseq.mrna.xeno yes # and genbank.est.native danRer11.genbank.mrna.xeno.load = yes danRer11.refseq.mrna.xeno.load = yes danRer11.downloadDir = danRer11 # danRer11.upstreamGeneTbl = refGene # danRer11.upstreamMaf = multiz7way # /hive/data/genomes/danRer10/bed/multiz7way/species.lst # ci1 (Ciona intestinalis) ci1.serverGenome = /hive/data/genomes/ci1/nib/Scaffold*.nib ci1.ooc = no ci1.maxIntron = 20000 ci1.lift = no ci1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ci1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ci1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ci1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ci1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} ci1.refseq.mrna.native.load = yes ci1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse ci1.genbank.mrna.xeno.load = yes ci1.downloadDir = ci1 ci1.perChromTables = no # ci2 (Ciona intestinalis) ci2.serverGenome = /hive/data/genomes/ci2/ci2.2bit ci2.ooc = /hive/data/genomes/ci2/11.ooc ci2.maxIntron = 20000 ci2.lift = no ci2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} ci2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} ci2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} ci2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} ci2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} ci2.refseq.mrna.native.load = yes ci2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse ci2.genbank.mrna.xeno.load = yes ci2.downloadDir = ci2 ci2.perChromTables = no # ci3 (Ciona intestinalis) ci3.serverGenome = /hive/data/genomes/ci3/ci3.2bit ci3.ooc = /hive/data/genomes/ci3/jkStuff/ci3.11.ooc ci3.maxIntron = 20000 ci3.lift = no ci3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} ci3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} ci3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} ci3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} ci3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} # refseq.mrna native and xeno are default yes # genbank.mrna and genbank.est native are default yes, the xeno is default no ci3.downloadDir = ci3 ci3.perChromTables = no # strPur1 (S. purpuratus) # 302 genbank mRNA # 219 refseq mRNA # 89289 genbank EST strPur1.serverGenome = /hive/data/genomes/strPur1/strPur1.2bit strPur1.ooc = /hive/data/genomes/strPur1/11.ooc strPur1.lift = no strPur1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} strPur1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} strPur1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} strPur1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} strPur1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} strPur1.refseq.mrna.native.load = yes strPur1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse strPur1.genbank.est.native.load = no strPur1.downloadDir = strPur1 strPur1.perChromTables = no # strPur2 (S. purpuratus) strPur2.serverGenome = /hive/data/genomes/strPur2/strPur2.2bit strPur2.ooc = /hive/data/genomes/strPur2/11.ooc strPur2.lift = no strPur2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} strPur2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} strPur2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} strPur2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} strPur2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} strPur2.refseq.mrna.native.load = yes strPur2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse strPur2.genbank.mrna.xeno.load = yes strPur2.genbank.est.native.load = yes strPur2.downloadDir = strPur2 strPur2.perChromTables = no # strPur4 (S. purpuratus) strPur4.serverGenome = /hive/data/genomes/strPur4/strPur4.2bit strPur4.ooc = /hive/data/genomes/strPur4/strPur4.11.ooc strPur4.lift = no strPur4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} strPur4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} strPur4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} strPur4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} strPur4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} strPur4.refseq.mrna.native.load = yes strPur4.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse strPur4.genbank.est.native.load = yes strPur4.downloadDir = strPur4 strPur4.perChromTables = no # canFam1 (dog) canFam1.serverGenome = /hive/data/genomes/canFam1/nib/chr*.nib canFam1.ooc = /hive/data/genomes/canFam1/11.ooc canFam1.align.unplacedChroms = chrUn canFam1.lift = /hive/data/genomes/canFam1/jkStuff/liftAll.lft canFam1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} canFam1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} canFam1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} canFam1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} canFam1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} canFam1.refseq.mrna.native.load = yes canFam1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse canFam1.downloadDir = canFam1 canFam1.upstreamGeneTbl = ensGene # canFam2 (dog) canFam2.serverGenome = /hive/data/genomes/canFam2/nib/chr*.nib canFam2.ooc = /hive/data/genomes/canFam2/11.ooc canFam2.lift = /hive/data/genomes/canFam2/jkStuff/liftAll.lft canFam2.align.unplacedChroms = chrUn canFam2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} canFam2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} canFam2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} canFam2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} canFam2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} canFam2.refseq.mrna.native.load = yes canFam2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse canFam2.genbank.mrna.xeno.load = yes canFam2.downloadDir = canFam2 canFam2.upstreamGeneTbl = refGene canFam2.upstreamMaf = multiz4way /hive/data/genomes/canFam2/bed/multiz4way/species.lst # canFam3 (dog) canFam3.serverGenome = /hive/data/genomes/canFam3/canFam3.2bit canFam3.ooc = /hive/data/genomes/canFam3/jkStuff/canFam3.11.ooc canFam3.lift = /hive/data/genomes/canFam3/jkStuff/canFam3.nonBridged.lift canFam3.align.unplacedChroms = chr* canFam3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} canFam3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} canFam3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} canFam3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} canFam3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} canFam3.refseq.mrna.native.load = yes canFam3.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse canFam3.genbank.mrna.xeno.load = yes canFam3.downloadDir = canFam3 canFam3.upstreamGeneTbl = refGene canFam3.perChromTables = no # canFam4 (German shepard - GCA_011100685.1 - UU_Cfam_GSD_1.0) canFam4.serverGenome = /hive/data/genomes/canFam4/canFam4.2bit canFam4.ooc = /hive/data/genomes/canFam4/jkStuff/canFam4.11.ooc canFam4.lift = /hive/data/genomes/canFam4/jkStuff/canFam4.nonBridged.lft canFam4.align.unplacedChroms = chrUn_* canFam4.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} canFam4.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} canFam4.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} canFam4.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} canFam4.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} canFam4.refseq.mrna.native.load = yes canFam4.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse canFam4.genbank.mrna.xeno.load = yes canFam4.downloadDir = canFam4 canFam4.upstreamGeneTbl = refGene canFam4.perChromTables = no # canFam5 (Great Dane - GCA_005444595.1 - UMICH_Zoey_3.1) canFam5.serverGenome = /hive/data/genomes/canFam5/canFam5.2bit canFam5.ooc = /hive/data/genomes/canFam5/jkStuff/canFam5.11.ooc canFam5.lift = /hive/data/genomes/canFam5/jkStuff/canFam5.5Kgaps.lft canFam5.align.unplacedChroms = chrUn_* canFam5.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} canFam5.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} canFam5.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} canFam5.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} canFam5.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} canFam5.refseq.mrna.native.load = yes canFam5.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse canFam5.genbank.mrna.xeno.load = yes canFam5.downloadDir = canFam5 canFam5.upstreamGeneTbl = refGene canFam5.perChromTables = no # ailMel1 (panda) ailMel1.serverGenome = /hive/data/genomes/ailMel1/ailMel1.2bit ailMel1.lift = no ailMel1.ooc = /hive/data/genomes/ailMel1/ailMel1.11.ooc ailMel1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ailMel1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ailMel1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ailMel1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ailMel1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} ailMel1.refseq.mrna.native.load = no ailMel1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse ailMel1.genbank.mrna.xeno.load = yes ailMel1.downloadDir = ailMel1 ailMel1.perChromTables = no ailMel1.upstreamGeneTbl = ensGene # droYak1 (D. yakuba) droYak1.serverGenome = /hive/data/genomes/droYak1/nib/chr*.nib droYak1.ooc = /hive/data/genomes/droYak1/11.ooc droYak1.lift = /hive/data/genomes/droYak1/jkStuff/liftAll.lft droYak1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droYak1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droYak1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droYak1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droYak1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droYak1.refseq.mrna.native.load = no droYak1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse droYak1.downloadDir = droYak1 # anoGam3 (A. gambiae) anoGam3.serverGenome = /hive/data/genomes/anoGam3/anoGam3.2bit anoGam3.ooc = /hive/data/genomes/anoGam3/jkStuff/anoGam3.11.ooc anoGam3.lift = /hive/data/genomes/anoGam3/jkStuff/nonBridged.lft anoGam3.perChromTables = no anoGam3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} anoGam3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} anoGam3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} anoGam3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} anoGam3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # anoGam1 had genbank.mrna.xeno.load as yes # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc anoGam3.genbank.mrna.xeno.load = yes anoGam3.downloadDir = anoGam3 # anoGam1 (A. gambiae) anoGam1.serverGenome = /hive/data/genomes/anoGam1/nib/chr*.nib anoGam1.ooc = /hive/data/genomes/anoGam1/11.ooc anoGam1.lift = /hive/data/genomes/anoGam1/jkStuff/liftAll.lft anoGam1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} anoGam1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} anoGam1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} anoGam1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} anoGam1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} anoGam1.refseq.mrna.native.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse anoGam1.genbank.mrna.xeno.load = yes anoGam1.downloadDir = anoGam1 # dp2 (D. pseudoobscura) dp2.serverGenome = /hive/data/genomes/dp2/nib/*.nib dp2.ooc = /hive/data/genomes/dp2/11.ooc dp2.lift = no dp2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} dp2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} dp2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} dp2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} dp2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} dp2.refseq.mrna.native.load = no dp2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse dp2.downloadDir = dp2 dp2.perChromTables = no # dp3 (D. pseudoobscura) dp3.serverGenome = /hive/data/genomes/dp3/nib/*.nib dp3.ooc = /hive/data/genomes/dp3/11.ooc dp3.lift = /hive/data/genomes/dp3/jkStuff/liftAll.lft dp3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} dp3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} dp3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} dp3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} dp3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} dp3.refseq.mrna.native.load = no dp3.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse dp3.genbank.est.native.load = yes dp3.downloadDir = dp3 # tetNig2 (Tetraodon) tetNig2.serverGenome = /hive/data/genomes/tetNig2/tetNig2.2bit tetNig2.ooc = /hive/data/genomes/tetNig2/tetNig2.11.ooc tetNig2.lift = /hive/data/genomes/tetNig2/tetNig2.contigs.lift tetNig2.align.unplacedChroms = chr*_random tetNig2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} tetNig2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} tetNig2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} tetNig2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} tetNig2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} tetNig2.downloadDir = tetNig2 tetNig2.genbank.est.native.load = no tetNig2.genbank.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse tetNig2.genbank.mrna.xeno.load = yes tetNig2.refseq.mrna.native.load = no tetNig2.upstreamGeneTbl = ensGene # tetNig1 (Tetraodon) tetNig1.serverGenome = /hive/data/genomes/tetNig1/nib/chr*.nib tetNig1.ooc = /hive/data/genomes/tetNig1/11.ooc tetNig1.lift = /hive/data/genomes/tetNig1/jkStuff/liftAll.lft tetNig1.align.unplacedChroms = chrUn_random tetNig1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} tetNig1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} tetNig1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} tetNig1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} tetNig1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} tetNig1.downloadDir = tetNig1 tetNig1.genbank.est.native.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse tetNig1.refseq.mrna.native.load = no tetNig1.upstreamGeneTbl = ensGene # poeRet1 (guppy) poeRet1.serverGenome = /hive/data/genomes/poeRet1/poeRet1.2bit poeRet1.ooc = /hive/data/genomes/poeRet1/jkStuff/poeRet1.11.ooc poeRet1.lift = /hive/data/genomes/poeRet1/jkStuff/poeRet1.nonBridged.lift poeRet1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} poeRet1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} poeRet1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} poeRet1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} poeRet1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} poeRet1.refseq.mrna.native.load = no poeRet1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse poeRet1.genbank.est.native.load = yes poeRet1.downloadDir = poeRet1 poeRet1.perChromTables = no # gasAcu1 (G. Aculeatus) gasAcu1.serverGenome = /hive/data/genomes/gasAcu1/gasAcu1.2bit gasAcu1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} gasAcu1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} gasAcu1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} gasAcu1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} gasAcu1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} gasAcu1.ooc = /hive/data/genomes/gasAcu1/11.ooc gasAcu1.lift = /hive/data/genomes/gasAcu1/jkStuff/liftAll.lft # DO NOT NEED genbank.mrna.xeno except for human, mouse gasAcu1.genbank.mrna.xeno.load = yes gasAcu1.downloadDir = gasAcu1 gasAcu1.upstreamGeneTbl = ensGene gasAcu1.upstreamMaf = multiz8way /hive/data/genomes/gasAcu1/bed/multiz8way/species.lst # chiLan1 (Chinchilla lanigera) chiLan1.serverGenome = /hive/data/genomes/chiLan1/chiLan1.2bit chiLan1.lift = no chiLan1.perChromTables = no chiLan1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} chiLan1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} chiLan1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} chiLan1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} chiLan1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} chiLan1.ooc = /hive/data/genomes/chiLan1/jkStuff/chiLan1.11.ooc chiLan1.refseq.mrna.native.load = yes chiLan1.refseq.mrna.xeno.load = yes chiLan1.genbank.mrna.xeno.load = no chiLan1.genbank.est.native.load = yes chiLan1.downloadDir = chiLan1 # musFur1 (Ferret, Mustela putorius furo, taxId 9669) musFur1.serverGenome = /hive/data/genomes/musFur1/musFur1.2bit musFur1.ooc = /hive/data/genomes/musFur1/jkStuff/musFur1.11.ooc musFur1.lift = no musFur1.perChromTables = no musFur1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} musFur1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} musFur1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} musFur1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} musFur1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} musFur1.refseq.mrna.native.load = yes musFur1.refseq.mrna.xeno.load = yes musFur1.genbank.mrna.xeno.load = no musFur1.genbank.est.native.load = yes musFur1.downloadDir = musFur1 # enhLutNer1 Enhydra lutris nereis (southern sea otter) (genbank assembly GCA_006410715.1) enhLutNer1.serverGenome = /hive/data/genomes/enhLutNer1/enhLutNer1.2bit enhLutNer1.ooc = /hive/data/genomes/enhLutNer1/jkStuff/enhLutNer1.11.ooc enhLutNer1.lift = no enhLutNer1.perChromTables = no enhLutNer1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} enhLutNer1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} enhLutNer1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} enhLutNer1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} enhLutNer1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} enhLutNer1.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} enhLutNer1.downloadDir = enhLutNer1 enhLutNer1.refseq.mrna.native.load = yes enhLutNer1.refseq.mrna.xeno.load = yes # oryLat2 (Oryzias latipes - Medaka) oryLat2.serverGenome = /hive/data/genomes/oryLat2/oryLat2.2bit oryLat2.lift = /hive/data/genomes/oryLat2/jkStuff/liftAll.lft oryLat2.perChromTables = no oryLat2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} oryLat2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} oryLat2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} oryLat2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} oryLat2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} oryLat2.ooc = /hive/data/genomes/oryLat2/11.ooc # DO NOT NEED genbank.mrna.xeno except for human, mouse oryLat2.genbank.mrna.xeno.load = yes oryLat2.refseq.mrna.native.load = yes oryLat2.refseq.mrna.xeno.load = yes oryLat2.downloadDir = oryLat2 oryLat2.upstreamGeneTbl = ensGene oryLat2.upstreamMaf = multiz5way /hive/data/genomes/oryLat2/bed/multiz5way/species.list # oryLat1 (Oryzias latipes - Medaka) oryLat1.serverGenome = /hive/data/genomes/oryLat1/oryLat1.2bit oryLat1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} oryLat1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} oryLat1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} oryLat1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} oryLat1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} oryLat1.ooc = /hive/data/genomes/oryLat1/11.ooc oryLat1.lift = /hive/data/genomes/oryLat1/jkStuff/liftAll.lft # DO NOT NEED genbank.mrna.xeno except for human, mouse oryLat1.refseq.mrna.native.load = no oryLat1.refseq.mrna.xeno.load = yes oryLat1.downloadDir = oryLat1 # oviAri4 (sheep - Ovis aries - refseq GCF_000298735.2 - taxId 9940) oviAri4.serverGenome = /hive/data/genomes/oviAri4/oviAri4.2bit oviAri4.ooc = /hive/data/genomes/oviAri4/jkStuff/oviAri4.11.ooc oviAri4.lift = no oviAri4.perChromTables = no oviAri4.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} oviAri4.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} oviAri4.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} oviAri4.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} oviAri4.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} oviAri4.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} oviAri4.downloadDir = oviAri4 # defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc # yes: genbank.est.native.load refseq.mrna.native.load # yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load # yes: refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc # no: genbank.est.native.loadDesc genbank.est.xeno.load # no: genbank.est.xeno.loadDesc # DO NOT NEED genbank.mrna.xeno except for human, mouse # have been doing this for chimp too: oviAri4.genbank.mrna.xeno.load = no # oviAri3 (Sheep) oviAri3.serverGenome = /hive/data/genomes/oviAri3/oviAri3.2bit oviAri3.ooc = /hive/data/genomes/oviAri3/jkStuff/oviAri3.11.ooc oviAri3.lift = no oviAri3.perChromTables = no oviAri3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} oviAri3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} oviAri3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} oviAri3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} oviAri3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} oviAri3.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} oviAri3.downloadDir = oviAri3 oviAri3.refseq.mrna.native.load = yes oviAri3.refseq.mrna.xeno.load = yes oviAri3.refseq.mrna.xeno.loadDesc = yes oviAri3.genbank.mrna.xeno.load = yes oviAri3.upstreamGeneTbl = refGene # oviAri1 (Sheep) oviAri1.serverGenome = /hive/data/genomes/oviAri1/oviAri1.2bit oviAri1.ooc = /hive/data/genomes/oviAri1/oviAri1.11.ooc oviAri1.lift = no oviAri1.perChromTables = no oviAri1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} oviAri1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} oviAri1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} oviAri1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} oviAri1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} oviAri1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} oviAri1.downloadDir = oviAri1 oviAri1.refseq.mrna.native.load = yes oviAri1.refseq.mrna.xeno.load = yes oviAri1.refseq.mrna.xeno.loadDesc = yes oviAri1.upstreamGeneTbl = refGene # otoGar3 (bushbaby) otoGar3.serverGenome = /hive/data/genomes/otoGar3/otoGar3.2bit otoGar3.ooc = /hive/data/genomes/otoGar3/jkStuff/otoGar3.11.ooc otoGar3.lift = no otoGar3.perChromTables = no otoGar3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} otoGar3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} otoGar3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} otoGar3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} otoGar3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} otoGar3.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} otoGar3.downloadDir = otoGar3 otoGar3.refseq.mrna.native.load = no otoGar3.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse otoGar3.genbank.mrna.xeno.load = yes otoGar3.genbank.mrna.xeno.loadDesc = no otoGar3.genbank.est.native.load = no # susScr11 (pig) susScr11.serverGenome = /hive/data/genomes/susScr11/susScr11.2bit susScr11.ooc = /hive/data/genomes/susScr11/jkStuff/susScr11.11.ooc susScr11.lift = /hive/data/genomes/susScr11/jkStuff/susScr11.nonBridged.lft susScr11.perChromTables = no susScr11.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} susScr11.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} susScr11.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} susScr11.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} susScr11.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} susScr11.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} susScr11.downloadDir = susScr11 susScr11.refseq.mrna.native.load = yes susScr11.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse susScr11.genbank.mrna.xeno.load = yes susScr11.genbank.mrna.xeno.loadDesc = no susScr11.genbank.est.native.load = yes # susScr11.upstreamGeneTbl = ensGene # susScr11.upstreamMaf = multiz12way # /hive/data/genomes/susScr11/bed/multiz12way/species.list # susScr3 (pig) susScr3.serverGenome = /hive/data/genomes/susScr3/susScr3.2bit susScr3.ooc = /hive/data/genomes/susScr3/jkStuff/susScr3.11.ooc susScr3.lift = /hive/data/genomes/susScr3/jkStuff/susScr3.nonBridged.lift susScr3.perChromTables = no susScr3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} susScr3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} susScr3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} susScr3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} susScr3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} susScr3.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} susScr3.downloadDir = susScr3 susScr3.refseq.mrna.native.load = yes susScr3.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse susScr3.genbank.mrna.xeno.load = yes susScr3.genbank.mrna.xeno.loadDesc = no susScr3.genbank.est.native.load = yes # susScr3.upstreamGeneTbl = ensGene # susScr3.upstreamMaf = multiz12way # /hive/data/genomes/susScr3/bed/multiz12way/species.list # susScr2 (Pig) susScr2.serverGenome = /hive/data/genomes/susScr2/susScr2.2bit susScr2.ooc = /hive/data/genomes/susScr2/susScr2.11.ooc susScr2.lift = /hive/data/genomes/susScr2/susScr2.nonBridged.lft susScr2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} susScr2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} susScr2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} susScr2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} susScr2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} susScr2.downloadDir = susScr2 susScr2.genbank.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse susScr2.genbank.mrna.xeno.load = yes susScr2.refseq.mrna.native.load = no susScr2.upstreamGeneTbl = ensGene # equCab3 (Equus caballus) equCab3.serverGenome = /hive/data/genomes/equCab3/equCab3.2bit equCab3.ooc = /hive/data/genomes/equCab3/jkStuff/equCab3.11.ooc equCab3.lift = no equCab3.downloadDir = equCab3 equCab3.perChromTables = no equCab3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} equCab3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} equCab3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} equCab3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} equCab3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} # defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc # yes: genbank.est.native.load refseq.mrna.native.load # yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load # yes: refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc # no: genbank.est.native.loadDesc genbank.est.xeno.load # no: genbank.est.xeno.loadDesc # DO NOT NEED genbank.mrna.xeno except for human, mouse # equCab3.upstreamGeneTbl = refGene # equCab3.upstreamMaf = multiz6way /hive/data/genomes/equCab3/bed/multiz6way/species.list # equCab2 (Equus caballus) equCab2.serverGenome = /hive/data/genomes/equCab2/equCab2.2bit equCab2.ooc = /hive/data/genomes/equCab2/equCab2.11.ooc equCab2.lift = /hive/data/genomes/equCab2/jkStuff/equCab2.chrUn.lift equCab2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} equCab2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} equCab2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} equCab2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} equCab2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} equCab2.align.unplacedChroms = chrUn equCab2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse equCab2.genbank.mrna.xeno.load = yes equCab2.downloadDir = equCab2 equCab2.upstreamGeneTbl = refGene # equCab2.upstreamMaf = multiz6way /hive/data/genomes/equCab2/bed/multiz6way/species.list # equCab1 (Equus caballus) equCab1.serverGenome = /hive/data/genomes/equCab1/equCab1.2bit equCab1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} equCab1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} equCab1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} equCab1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} equCab1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} equCab1.ooc = /hive/data/genomes/equCab1/11.ooc equCab1.lift = /hive/data/genomes/equCab1/jkStuff/genbank.lft equCab1.align.unplacedChroms = chrUn # DO NOT NEED genbank.mrna.xeno except for human, mouse equCab1.genbank.mrna.xeno.load = yes equCab1.downloadDir = equCab1 equCab1.upstreamGeneTbl = refGene # cerSim1 (Ceratotherium simum - White Rhino) cerSim1.serverGenome = /hive/data/genomes/cerSim1/cerSim1.2bit cerSim1.ooc = /hive/data/genomes/cerSim1/jkStuff/cerSim1.11.ooc cerSim1.lift = no cerSim1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} cerSim1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} cerSim1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} cerSim1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} cerSim1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} cerSim1.refseq.mrna.native.load = no cerSim1.refseq.mrna.xeno.load = yes cerSim1.genbank.mrna.xeno.load = no cerSim1.genbank.est.native.load = no cerSim1.downloadDir = cerSim1 cerSim1.perChromTables = no # Nov 2017 (GSC) at Washington University (WashU) School of Medicine # Felis_catus_9.0 # felCat9 (Cat) felCat9.serverGenome = /hive/data/genomes/felCat9/felCat9.2bit felCat9.ooc = /hive/data/genomes/felCat9/jkStuff/felCat9.11.ooc felCat9.lift = /hive/data/genomes/felCat9/jkStuff/felCat9.nonBridged.lft felCat9.perChromTables = no felCat9.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} felCat9.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} felCat9.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} felCat9.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} felCat9.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} felCat9.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} felCat9.genbank.mrna.xeno.load = yes felCat9.downloadDir = felCat9 felCat9.refseq.mrna.native.load = yes felCat9.refseq.mrna.xeno.load = yes felCat9.refseq.mrna.xeno.loadDesc = yes # felCat9.upstreamGeneTbl = refGene # felCat9.upstreamMaf = multiz6way # /hive/data/genomes/felCat9/bed/multiz6way/species.list # Nov. 2014 International Cat Genome Sequencing Consortium Felis_catus_8.0 # felCat8 (Cat) felCat8.serverGenome = /hive/data/genomes/felCat8/felCat8.2bit felCat8.ooc = /hive/data/genomes/felCat8/jkStuff/felCat8.11.ooc felCat8.lift = /hive/data/genomes/felCat8/jkStuff/felCat8.nonBridged.lift felCat8.perChromTables = no felCat8.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} felCat8.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} felCat8.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} felCat8.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} felCat8.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} felCat8.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} felCat8.genbank.mrna.xeno.load = yes felCat8.downloadDir = felCat8 felCat8.refseq.mrna.native.load = yes felCat8.refseq.mrna.xeno.load = yes felCat8.refseq.mrna.xeno.loadDesc = yes # felCat8.upstreamGeneTbl = refGene # felCat8.upstreamMaf = multiz6way /hive/data/genomes/felCat8/bed/multiz6way/species.list # felCat5 felCat5.serverGenome = /hive/data/genomes/felCat5/felCat5.2bit felCat5.ooc = /hive/data/genomes/felCat5/jkStuff/felCat5.11.ooc felCat5.lift = /hive/data/genomes/felCat5/jkStuff/felCat5.nonBridged.lift felCat5.perChromTables = no felCat5.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} felCat5.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} felCat5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} felCat5.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} felCat5.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} felCat5.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} felCat5.genbank.mrna.xeno.load = yes felCat5.downloadDir = felCat5 felCat5.refseq.mrna.native.load = yes felCat5.refseq.mrna.xeno.load = yes felCat5.refseq.mrna.xeno.loadDesc = yes # felCat5.upstreamGeneTbl = refGene # felCat5.upstreamMaf = multiz6way /hive/data/genomes/felCat5/bed/multiz6way/species.list # felCat4 felCat4.serverGenome = /hive/data/genomes/felCat4/felCat4.2bit felCat4.ooc = /hive/data/genomes/felCat4/felCat4.11.ooc felCat4.lift = no felCat4.perChromTables = no felCat4.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} felCat4.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} felCat4.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} felCat4.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} felCat4.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} felCat4.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} felCat4.downloadDir = felCat4 felCat4.refseq.mrna.native.load = yes felCat4.refseq.mrna.xeno.load = yes felCat4.refseq.mrna.xeno.loadDesc = yes felCat4.upstreamGeneTbl = refGene felCat4.upstreamMaf = multiz6way /hive/data/genomes/felCat4/bed/multiz6way/species.list # felCat3 (cat) 217790 scaffolds felCat3.serverGenome = /hive/data/genomes/felCat3/felCat3.2bit felCat3.ooc = /hive/data/genomes/felCat3/11.ooc felCat3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} felCat3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} felCat3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} felCat3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} felCat3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} felCat3.lift = no felCat3.refseq.mrna.xeno.load = yes felCat3.downloadDir = felCat3 felCat3.perChromTables = no felCat3.upstreamGeneTbl = ensGene felCat3.upstreamMaf = multiz4way /hive/data/genomes/felCat3/bed/multiz4way/species.lst # bisBis1 (Bison) 450182 contigs bisBis1.serverGenome = /hive/data/genomes/bisBis1/bisBis1.2bit bisBis1.ooc = /hive/data/genomes/bisBis1/jkStuff/bisBis1.11.ooc bisBis1.lift = no bisBis1.perChromTables = no bisBis1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} bisBis1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} bisBis1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} bisBis1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} bisBis1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} bisBis1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} bisBis1.downloadDir = bisBis1 bisBis1.refseq.mrna.native.load = yes bisBis1.refseq.mrna.xeno.load = yes bisBis1.refseq.mrna.xeno.loadDesc = yes bisBis1.genbank.mrna.native.load = no bisBis1.genbank.mrna.native.loadDesc = no # DO NOT NEED genbank.mrna.xeno except for human, mouse bisBis1.genbank.mrna.xeno.load = no bisBis1.genbank.mrna.xeno.loadDesc = no bisBis1.genbank.est.native.load = no bisBis1.genbank.est.native.loadDesc = no # bisBis1.upstreamGeneTbl = ensGene # bosTau2 (B. taurus) 30 chromosomes plus 98058 scaffolds # Lift file partitions unplaced sequence pseudo-chroms bosTau2.serverGenome = /hive/data/genomes/bosTau2/bosTau2.2bit bosTau2.ooc = /hive/data/genomes/bosTau2/11.ooc bosTau2.lift = /hive/data/genomes/bosTau2/downloads/chrBin0.lft bosTau2.align.unplacedChroms = chrBin0 bosTau2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} bosTau2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} bosTau2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} bosTau2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} bosTau2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} bosTau2.refseq.mrna.native.load = yes bosTau2.refseq.mrna.xeno.load = yes bosTau2.downloadDir = bosTau2 bosTau2.perChromTables = no bosTau2.mgc = yes bosTau2.upstreamGeneTbl = refGene # bosTau3 (B. taurus) 30 chromosomes plus 13045 scaffolds bosTau3.serverGenome = /hive/data/genomes/bosTau3/bosTau3.2bit bosTau3.ooc = /hive/data/genomes/bosTau3/11.ooc bosTau3.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} bosTau3.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} bosTau3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} bosTau3.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} bosTau3.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} bosTau3.lift = no bosTau3.downloadDir = bosTau3 bosTau3.perChromTables = no bosTau3.mgc = yes bosTau3.upstreamGeneTbl = refGene # bosTau4 (B. taurus) 31 chromosomes plus 11869 scaffolds bosTau4.serverGenome = /hive/data/genomes/bosTau4/bosTau4.2bit bosTau4.ooc = /hive/data/genomes/bosTau4/bosTau4.11.ooc bosTau4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} bosTau4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} bosTau4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} bosTau4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} bosTau4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} bosTau4.lift = no bosTau4.downloadDir = bosTau4 bosTau4.perChromTables = no bosTau4.mgc = yes bosTau4.upstreamGeneTbl = mgcGenes bosTau4.upstreamMaf = multiz5way /hive/data/genomes/bosTau4/bed/multiz5way/species.list # bosTau6 (Cow) bosTau6.serverGenome = /hive/data/genomes/bosTau6/bosTau6.2bit bosTau6.ooc = /hive/data/genomes/bosTau6/bosTau6.11.ooc bosTau6.lift = no bosTau6.perChromTables = no bosTau6.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} bosTau6.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} bosTau6.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} bosTau6.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} bosTau6.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} bosTau6.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} bosTau6.downloadDir = bosTau6 bosTau6.refseq.mrna.native.load = yes bosTau6.refseq.mrna.xeno.load = yes bosTau6.refseq.mrna.xeno.loadDesc = yes bosTau6.genbank.mrna.xeno.load = yes bosTau6.upstreamGeneTbl = refGene # bosTau7 (Cow) bosTau7.serverGenome = /hive/data/genomes/bosTau7/bosTau7.2bit bosTau7.ooc = /hive/data/genomes/bosTau7/bosTau7.11.ooc bosTau7.lift = no bosTau7.perChromTables = no bosTau7.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} bosTau7.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} bosTau7.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} bosTau7.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} bosTau7.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} bosTau7.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} bosTau7.downloadDir = bosTau7 bosTau7.refseq.mrna.native.load = yes bosTau7.refseq.mrna.xeno.load = yes bosTau7.refseq.mrna.xeno.loadDesc = yes bosTau7.genbank.mrna.xeno.load = yes bosTau7.upstreamGeneTbl = refGene bosTau8.serverGenome = /hive/data/genomes/bosTau8/bosTau8.2bit bosTau8.ooc = /hive/data/genomes/bosTau8/bosTau8.11.ooc bosTau8.lift = no bosTau8.perChromTables = no bosTau8.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} bosTau8.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} bosTau8.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} bosTau8.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} bosTau8.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} bosTau8.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} bosTau8.downloadDir = bosTau8 bosTau8.refseq.mrna.native.load = yes bosTau8.refseq.mrna.xeno.load = yes bosTau8.refseq.mrna.xeno.loadDesc = yes bosTau8.upstreamGeneTbl = refGene # bosTau9 (cow - Bos taurus - refseq GCF_002263795.1 ARS-UCD1.2 - taxId 9913) bosTau9.serverGenome = /hive/data/genomes/bosTau9/bosTau9.2bit bosTau9.ooc = /hive/data/genomes/bosTau9/jkStuff/bosTau9.11.ooc bosTau9.lift = no bosTau9.perChromTables = no bosTau9.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} bosTau9.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} bosTau9.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} bosTau9.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} bosTau9.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} bosTau9.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} bosTau9.downloadDir = bosTau9 # bosTau9.upstreamGeneTbl = refGene # defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc # yes: genbank.est.native.load refseq.mrna.native.load # yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load # yes: refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc # no: genbank.est.native.loadDesc genbank.est.xeno.load # no: genbank.est.xeno.loadDesc +# ambMex2 (Axolotl - Ambystoma mexicanum) GCA_002915635.2 - 30Gb total +ambMex2.serverGenome = /hive/data/genomes/ambMex2/ambMex2.2bit +ambMex2.ooc = /hive/data/genomes/ambMex2/jkStuff/ambMex2.11.ooc +ambMex2.lift = /hive/data/genomes/ambMex2/jkStuff/ambMex2.100baseGaps.lft +ambMex2.perChromTables = no +ambMex2.downloadDir = ambMex2 +ambMex2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} +ambMex2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} +ambMex2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} +ambMex2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} +ambMex2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} +ambMex2.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} +# defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc +# yes: genbank.est.native.load refseq.mrna.native.load +# yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load +# yes: refseq.mrna.xeno.loadDesc +# defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc +# no: genbank.est.native.loadDesc genbank.est.xeno.load +# no: genbank.est.xeno.loadDesc +# DO NOT NEED genbank.mrna.xeno except for human, mouse +# ambMex2.upstreamGeneTbl = ensGene +# ambMex2.upstreamMaf = multiz6way /hive/data/genomes/ambMex2/bed/multiz6way/species.list + + # ambMex1 (Axolotl - Ambystoma mexicanum) 125724 scaffolds N50 3052786 - 30Gb total ambMex1.serverGenome = /hive/data/genomes/ambMex1/ambMex1.2bit ambMex1.ooc = /hive/data/genomes/ambMex1/jkStuff/ambMex1.11.ooc ambMex1.lift = /hive/data/genomes/ambMex1/jkStuff/ambMex1.10Kgaps.lft ambMex1.perChromTables = no ambMex1.downloadDir = ambMex1 ambMex1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ambMex1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ambMex1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ambMex1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ambMex1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} ambMex1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} # defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc # yes: genbank.est.native.load refseq.mrna.native.load # yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load # yes: refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc # no: genbank.est.native.loadDesc genbank.est.xeno.load # no: genbank.est.xeno.loadDesc # DO NOT NEED genbank.mrna.xeno except for human, mouse # ambMex1.upstreamGeneTbl = ensGene # ambMex1.upstreamMaf = multiz6way /hive/data/genomes/ambMex1/bed/multiz6way/species.list # nanPar1 (tibetan frog) 25187 scaffolds N50 1069101 nanPar1.serverGenome = /hive/data/genomes/nanPar1/nanPar1.2bit nanPar1.ooc = /hive/data/genomes/nanPar1/jkStuff/nanPar1.11.ooc nanPar1.lift = no nanPar1.perChromTables = no nanPar1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} nanPar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} nanPar1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} nanPar1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} nanPar1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} nanPar1.downloadDir = nanPar1 nanPar1.refseq.mrna.native.load = no nanPar1.refseq.mrna.xeno.load = yes nanPar1.refseq.mrna.xeno.loadDesc = yes nanPar1.genbank.mrna.native.load = no nanPar1.genbank.mrna.native.loadDesc = no # DO NOT NEED genbank.mrna.xeno except for human, mouse nanPar1.genbank.est.native.load = no nanPar1.genbank.est.native.loadDesc = no # nanPar1.upstreamGeneTbl = ensGene # xenLae2 'Xenopus laevis' 19 chroms + 108014 contigs xenLae2.serverGenome = /hive/data/genomes/xenLae2/xenLae2.2bit xenLae2.ooc = /hive/data/genomes/xenLae2/jkStuff/xenLae2.11.ooc xenLae2.lift = no xenLae2.perChromTables = no xenLae2.downloadDir = xenLae2 # xenLae2.mgc = yes xenLae2.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} xenLae2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} xenLae2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} xenLae2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} xenLae2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc # xenLae2.upstreamGeneTbl = ensGene # xenLae2.upstreamMaf = multiz9way /hive/data/genomes/xenTro7/bed/multiz9way/species.list # xenTro9 'Xenopus tropicalis' 11 chroms + 6811 contigs xenTro9.serverGenome = /hive/data/genomes/xenTro9/xenTro9.2bit xenTro9.ooc = /hive/data/genomes/xenTro9/jkStuff/xenTro9.11.ooc xenTro9.lift = no xenTro9.perChromTables = no xenTro9.downloadDir = xenTro9 # xenTro9.mgc = yes xenTro9.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} xenTro9.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} xenTro9.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} xenTro9.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} xenTro9.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc # xenTro9.upstreamGeneTbl = ensGene # xenTro9.upstreamMaf = multiz9way /hive/data/genomes/xenTro7/bed/multiz9way/species.list # xenTro7 'Xenopus tropicalis' 7728 scaffolds xenTro7.serverGenome = /hive/data/genomes/xenTro7/xenTro7.2bit xenTro7.ooc = /hive/data/genomes/xenTro7/jkStuff/xenTro7.11.ooc xenTro7.lift = no xenTro7.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} xenTro7.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} xenTro7.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} xenTro7.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} xenTro7.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} xenTro7.refseq.mrna.native.load = yes xenTro7.genbank.est.native.load = yes xenTro7.refseq.mrna.xeno.load = yes xenTro7.refseq.mrna.xeno.loadDesc = yes xenTro7.genbank.mrna.xeno.load = no xenTro7.downloadDir = xenTro7 xenTro7.perChromTables = no xenTro7.mgc = yes # xenTro7.upstreamGeneTbl = ensGene # xenTro7.upstreamMaf = multiz9way /hive/data/genomes/xenTro7/bed/multiz9way/species.list # xenTro3 (X. tropicalis) 19550 scaffolds xenTro3.serverGenome = /hive/data/genomes/xenTro3/xenTro3.2bit xenTro3.ooc = /hive/data/genomes/xenTro3/xenTro3.11.ooc xenTro3.lift = no xenTro3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} xenTro3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} xenTro3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} xenTro3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} xenTro3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} xenTro3.refseq.mrna.native.load = yes xenTro3.genbank.est.native.load = yes xenTro3.refseq.mrna.xeno.load = no xenTro3.genbank.mrna.xeno.load = no xenTro3.downloadDir = xenTro3 xenTro3.perChromTables = no xenTro3.mgc = yes xenTro3.upstreamGeneTbl = ensGene xenTro3.upstreamMaf = multiz9way /hive/data/genomes/xenTro3/bed/multiz9way/species.list # xenTro2 (X. tropicalis) 19579 scaffolds xenTro2.serverGenome = /hive/data/genomes/xenTro2/xenTro2.2bit xenTro2.ooc = /hive/data/genomes/xenTro2/11.ooc xenTro2.lift = no xenTro2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} xenTro2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} xenTro2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} xenTro2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} xenTro2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} xenTro2.refseq.mrna.native.load = yes xenTro2.genbank.mrna.xeno.load = no xenTro2.downloadDir = xenTro2 xenTro2.perChromTables = no xenTro2.mgc = yes xenTro2.upstreamGeneTbl = mgcGenes xenTro2.upstreamMaf = multiz7way /hive/data/genomes/xenTro2/bed/multiz7way/species.lst # xenTro1 (X. tropicalis) 27064 scaffolds! xenTro1.serverGenome = /hive/data/genomes/xenTro1/xenTro1.2bit xenTro1.ooc = /hive/data/genomes/xenTro1/11.ooc xenTro1.lift = no xenTro1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} xenTro1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} xenTro1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} xenTro1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} xenTro1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} xenTro1.refseq.mrna.native.load = no xenTro1.genbank.mrna.xeno.load = no xenTro1.downloadDir = xenTro1 xenTro1.perChromTables = no xenTro1.mgc = yes xenTro1.upstreamGeneTbl = mgcGenes xenTro1.upstreamMaf = multiz5way /hive/data/genomes/xenTro1/bed/multiz/species.lst # anoCar2 (A. carolinensis) anoCar2.serverGenome = /hive/data/genomes/anoCar2/anoCar2.2bit anoCar2.ooc = /hive/data/genomes/anoCar2/anoCar2.11.ooc anoCar2.lift = /hive/data/genomes/anoCar2/nonBridged.lift anoCar2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} anoCar2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} anoCar2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} anoCar2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} anoCar2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} anoCar2.refseq.mrna.native.load = no anoCar2.genbank.est.native.load = yes anoCar2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse anoCar2.genbank.mrna.xeno.load = yes anoCar2.downloadDir = anoCar2 anoCar2.perChromTables = no anoCar2.upstreamGeneTbl = ensGene anoCar2.upstreamMaf = multiz7way /hive/data/genomes/anoCar2/bed/multiz7way/species.list # anoCar1 (A. carolinensis) anoCar1.serverGenome = /hive/data/genomes/anoCar1/anoCar1.2bit anoCar1.ooc = /hive/data/genomes/anoCar1/11.ooc anoCar1.lift = no anoCar1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} anoCar1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} anoCar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} anoCar1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} anoCar1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} anoCar1.refseq.mrna.native.load = no anoCar1.genbank.est.native.load = no anoCar1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse anoCar1.downloadDir = anoCar1 anoCar1.perChromTables = no anoCar1.upstreamGeneTbl = ensGene # thaSir1 (Thamnophis sirtalis/Garter snake taxId 35019 GCF_001077635.1) # 7930 contigs thaSir1.serverGenome = /hive/data/genomes/thaSir1/thaSir1.2bit thaSir1.ooc = /hive/data/genomes/thaSir1/jkStuff/thaSir1.11.ooc thaSir1.lift = no thaSir1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} thaSir1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} thaSir1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} thaSir1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} thaSir1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} thaSir1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} # defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc # yes: genbank.est.native.load refseq.mrna.native.load # yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load # yes: refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc # no: genbank.est.native.loadDesc genbank.est.xeno.load # no: genbank.est.xeno.loadDesc # DO NOT NEED genbank.mrna.xeno except for human, mouse thaSir1.downloadDir = thaSir1 thaSir1.perChromTables = no # thaSir1.upstreamGeneTbl = ensGene # macEug1 (wallaby) macEug1.serverGenome = /hive/data/genomes/macEug1/macEug1.2bit macEug1.ooc = /hive/data/genomes/macEug1/macEug1.11.ooc macEug1.lift = no macEug1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} macEug1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} macEug1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} macEug1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} macEug1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} macEug1.refseq.mrna.native.load = no macEug1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse macEug1.genbank.est.native.load = no macEug1.downloadDir = macEug1 macEug1.perChromTables = no macEug1.upstreamGeneTbl = xenoRefGene # macEug2 (wallaby) macEug2.serverGenome = /hive/data/genomes/macEug2/macEug2.2bit macEug2.ooc = /hive/data/genomes/macEug2/macEug2.11.ooc macEug2.lift = no macEug2.perChromTables = no macEug2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} macEug2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} macEug2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} macEug2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} macEug2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} macEug2.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} macEug2.downloadDir = macEug2 macEug2.refseq.mrna.native.load = no macEug2.refseq.mrna.xeno.load = yes macEug2.refseq.mrna.xeno.loadDesc = yes macEug2.genbank.est.native.load = yes macEug2.genbank.est.native.loadDesc = yes macEug2.genbank.mrna.native.load = yes macEug2.genbank.mrna.native.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse macEug2.genbank.est.native.load = yes macEug2.genbank.est.native.loadDesc = yes # triMan1 (manatee) triMan1.serverGenome = /hive/data/genomes/triMan1/triMan1.2bit triMan1.ooc = /hive/data/genomes/triMan1/jkStuff/triMan1.11.ooc triMan1.lift = no triMan1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} triMan1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} triMan1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} triMan1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} triMan1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} triMan1.refseq.mrna.native.load = no triMan1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse triMan1.genbank.est.native.load = no triMan1.downloadDir = triMan1 triMan1.perChromTables = no # dasNov1 (armadillo) dasNov1.serverGenome = /hive/data/genomes/dasNov1/dasNov1.2bit dasNov1.ooc = /hive/data/genomes/dasNov1/11.ooc dasNov1.lift = no dasNov1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} dasNov1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} dasNov1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} dasNov1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} dasNov1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} dasNov1.refseq.mrna.native.load = no dasNov1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse dasNov1.genbank.est.native.load = no dasNov1.downloadDir = dasNov1 dasNov1.perChromTables = no # loxAfr3 (elephant) loxAfr3.serverGenome = /hive/data/genomes/loxAfr3/loxAfr3.2bit loxAfr3.ooc = /hive/data/genomes/loxAfr3/loxAfr3.11.ooc loxAfr3.lift = no loxAfr3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} loxAfr3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} loxAfr3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} loxAfr3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} loxAfr3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} loxAfr3.refseq.mrna.native.load = yes loxAfr3.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse loxAfr3.genbank.mrna.xeno.load = yes loxAfr3.genbank.est.native.load = no loxAfr3.downloadDir = loxAfr3 loxAfr3.perChromTables = no loxAfr3.upstreamGeneTbl = ensGene # loxAfr1 (elephant) loxAfr1.serverGenome = /hive/data/genomes/loxAfr1/loxAfr1.2bit loxAfr1.ooc = /hive/data/genomes/loxAfr1/11.ooc loxAfr1.lift = no loxAfr1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} loxAfr1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} loxAfr1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} loxAfr1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} loxAfr1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} loxAfr1.refseq.mrna.native.load = no loxAfr1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse loxAfr1.genbank.est.native.load = no loxAfr1.downloadDir = loxAfr1 loxAfr1.perChromTables = no # echTel2 (tenrec) echTel2.serverGenome = /hive/data/genomes/echTel2/echTel2.2bit echTel2.ooc = /hive/data/genomes/echTel2/jkStuff/echTel2.11.ooc echTel2.lift = no echTel2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} echTel2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} echTel2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} echTel2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} echTel2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} echTel2.refseq.mrna.native.load = no echTel2.refseq.mrna.xeno.load = yes echTel2.genbank.mrna.xeno.load = no echTel2.genbank.est.native.load = no echTel2.genbank.mrna.native.load = no echTel2.genbank.mrna.native.loadDesc = no echTel2.downloadDir = echTel2 echTel2.perChromTables = no # echTel1 (tenrec) echTel1.serverGenome = /hive/data/genomes/echTel1/echTel1.2bit echTel1.ooc = /hive/data/genomes/echTel1/jkStuff/echTel1.11.ooc echTel1.lift = no echTel1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} echTel1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} echTel1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} echTel1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} echTel1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} echTel1.refseq.mrna.native.load = no echTel1.refseq.mrna.xeno.load = yes echTel1.genbank.mrna.xeno.load = no echTel1.genbank.est.native.load = no echTel1.genbank.mrna.native.load = no echTel1.genbank.mrna.native.loadDesc = no echTel1.downloadDir = echTel1 echTel1.perChromTables = no # oryCun2 (rabbit) oryCun2.serverGenome = /hive/data/genomes/oryCun2/oryCun2.2bit oryCun2.ooc = /hive/data/genomes/oryCun2/oryCun2.11.ooc oryCun2.lift = /hive/data/genomes/oryCun2/oryCun2.contigs.lift oryCun2.perChromTables = no oryCun2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} oryCun2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} oryCun2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} oryCun2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} oryCun2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} oryCun2.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} oryCun2.downloadDir = oryCun2 oryCun2.refseq.mrna.native.load = yes oryCun2.refseq.mrna.xeno.load = yes oryCun2.refseq.mrna.xeno.loadDesc = yes oryCun2.genbank.mrna.xeno.load = yes oryCun2.upstreamGeneTbl = xenoRefGene # oryCun1 (rabbit) oryCun1.serverGenome = /hive/data/genomes/oryCun1/oryCun1.2bit oryCun1.ooc = no oryCun1.lift = no oryCun1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} oryCun1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} oryCun1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} oryCun1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} oryCun1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} oryCun1.refseq.mrna.native.load = no oryCun1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse oryCun1.genbank.est.native.load = yes oryCun1.downloadDir = oryCun1 oryCun1.perChromTables = no # cavApe1 Cavia aperea (Brazilian guinea pig) taxId: 37548 cavApe1.serverGenome = /hive/data/genomes/cavApe1/cavApe1.2bit cavApe1.ooc = /hive/data/genomes/cavApe1/jkStuff/cavApe1.11.ooc cavApe1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} cavApe1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} cavApe1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} cavApe1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} cavApe1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} cavApe1.lift = /hive/data/genomes/cavApe1/jkStuff/nonBridged.lft cavApe1.downloadDir = cavApe1 cavApe1.perChromTables = no # there are no native anything cavApe1.refseq.mrna.native.load = no cavApe1.refseq.mrna.native.loadDesc = no cavApe1.genbank.mrna.native.load = no cavApe1.genbank.mrna.native.loadDesc = no # defaults yes: genbank.mrna.native.load and loadDesc # defaults yes: genbank.est.native.load # defaults yes: refseq.mrna.native.load, refseq.mrna.native.loadDesc # defaults yes: refseq.mrna.xeno.load, refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load and loadDesc # defaults no: genbank.est.xeno.load, genbank.est.xeno.loadDesc # DO NOT NEED genbank.mrna.xeno except for human, mouse # cavPor3 (C. porcellus) 3144 scaffolds 967 are multi-contig and 2076 are single contig cavPor3.serverGenome = /hive/data/genomes/cavPor3/cavPor3.2bit cavPor3.ooc = /hive/data/genomes/cavPor3/cavPor3.11.ooc cavPor3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} cavPor3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} cavPor3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} cavPor3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} cavPor3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} cavPor3.lift = no cavPor3.downloadDir = cavPor3 cavPor3.perChromTables = no cavPor3.refseq.mrna.native.load = yes cavPor3.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse cavPor3.genbank.mrna.xeno.load = yes cavPor3.genbank.est.native.load = yes cavPor3.upstreamGeneTbl = xenoRefGene cavPor3.upstreamMaf = multiz8way /hive/data/genomes/cavPor3/bed/multiz8way/species.list # ornAna2 (Platypus -- Ornithorhynchus anatinus) ornAna2.serverGenome = /hive/data/genomes/ornAna2/ornAna2.2bit ornAna2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ornAna2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ornAna2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ornAna2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ornAna2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} ornAna2.ooc = /hive/data/genomes/ornAna2/jkStuff/ornAna2.11.ooc ornAna2.lift = no ornAna2.refseq.mrna.xeno.load = yes ornAna2.refseq.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse ornAna2.genbank.mrna.xeno.load = no ornAna2.downloadDir = ornAna2 ornAna2.perChromTables = no # ornAna2.upstreamGeneTbl = ensGene # ornAna2.upstreamMaf = multiz6way /hive/data/genomes/ornAna1/bed/multiz6way.2007-04-24/species.lst # ornAna1 (Platypus -- O. anatinus) ornAna1.serverGenome = /hive/data/genomes/ornAna1/ornAna1.2bit ornAna1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ornAna1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ornAna1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ornAna1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ornAna1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} ornAna1.ooc = /hive/data/genomes/ornAna1/11.ooc ornAna1.lift = no ornAna1.refseq.mrna.xeno.load = yes ornAna1.refseq.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse ornAna1.genbank.mrna.xeno.load = yes ornAna1.downloadDir = ornAna1 ornAna1.perChromTables = no ornAna1.upstreamGeneTbl = ensGene ornAna1.upstreamMaf = multiz6way /hive/data/genomes/ornAna1/bed/multiz6way.2007-04-24/species.lst # petMar3 (Petromyzon marinus - Sea Lamprey - taxId 7757) petMar3.serverGenome = /hive/data/genomes/petMar3/petMar3.2bit petMar3.ooc = /hive/data/genomes/petMar3/jkStuff/petMar3.11.ooc petMar3.lift = no petMar3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} petMar3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} petMar3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} petMar3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} petMar3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} # defaults yes: genbank.mrna.native.load and loadDesc # defaults yes: genbank.est.native.load # defaults yes: refseq.mrna.native.load, refseq.mrna.native.loadDesc # defaults yes: refseq.mrna.xeno.load, refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load and loadDesc # defaults no: genbank.est.xeno.load, genbank.est.xeno.loadDesc # DO NOT NEED genbank.mrna.xeno except for human, mouse petMar3.downloadDir = petMar3 petMar3.perChromTables = no # petMar2 (Petromyzon marinus - Sea Lamprey) petMar2.serverGenome = /hive/data/genomes/petMar2/petMar2.2bit petMar2.ooc = /hive/data/genomes/petMar2/jkStuff/petMar2.11.ooc petMar2.lift = no petMar2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} petMar2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} petMar2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} petMar2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} petMar2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} petMar2.refseq.mrna.native.load = yes petMar2.refseq.mrna.xeno.load = yes petMar2.genbank.mrna.xeno.load = no petMar2.genbank.est.native.load = yes petMar2.downloadDir = petMar2 petMar2.perChromTables = no petMar2.upstreamGeneTbl = xenoRefGene petMar2.upstreamMaf = multiz7way /hive/data/genomes/petMar2/bed/multiz7way/species.list # petMar1 (Petromyzon marinus - Sea Lamprey) petMar1.serverGenome = /hive/data/genomes/petMar1/petMar1.2bit petMar1.ooc = /hive/data/genomes/petMar1/petMar1.11.ooc petMar1.lift = no petMar1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} petMar1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} petMar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} petMar1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} petMar1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} petMar1.refseq.mrna.native.load = yes petMar1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse petMar1.genbank.mrna.xeno.load = yes petMar1.genbank.est.native.load = yes petMar1.downloadDir = petMar1 petMar1.perChromTables = no petMar1.upstreamGeneTbl = xenoRefGene petMar1.upstreamMaf = multiz6way /hive/data/genomes/petMar1/bed/multiz6way/species.list # braFlo2 (Branchiostoma floridae - Lancelet) braFlo2.serverGenome = /hive/data/genomes/braFlo2/braFlo2.2bit braFlo2.ooc = /hive/data/genomes/braFlo2/jkStuff/braFlo2.11.ooc braFlo2.lift = /hive/data/genomes/braFlo2/jkStuff/braFlo2.nonBridged.lift braFlo2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} braFlo2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} braFlo2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} braFlo2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} braFlo2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} braFlo2.refseq.mrna.native.load = yes braFlo2.refseq.mrna.xeno.load = yes braFlo2.genbank.mrna.xeno.load = no braFlo2.genbank.est.native.load = yes braFlo2.downloadDir = braFlo2 braFlo2.perChromTables = no # braFlo1 (Branchiostoma floridae - Lancelet) braFlo1.serverGenome = /hive/data/genomes/braFlo1/braFlo1.2bit braFlo1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} braFlo1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} braFlo1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} braFlo1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} braFlo1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} braFlo1.ooc = /hive/data/genomes/braFlo1/11.ooc braFlo1.lift = /hive/data/genomes/braFlo1/jkStuff/liftAll.lft braFlo1.refseq.mrna.native.load = no braFlo1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse braFlo1.genbank.mrna.xeno.load = yes braFlo1.genbank.est.native.load = yes braFlo1.downloadDir = braFlo1 braFlo1.perChromTables = no braFlo1.upstreamGeneTbl = xenoRefGene braFlo1.upstreamMaf = multiz5way /hive/data/genomes/braFlo1/bed/multiz5way/species.list # oxyTri2 (Oxytricha trifallax) oxyTri2.serverGenome = /hive/data/genomes/oxyTri2/oxyTri2.2bit oxyTri2.ooc = /hive/data/genomes/oxyTri2/jkStuff/oxyTri2.11.ooc oxyTri2.lift = /hive/data/genomes/oxyTri2/jkStuff/oxyTri2.nonBridged.lft oxyTri2.perChromTables = no oxyTri2.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} oxyTri2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} oxyTri2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} oxyTri2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} oxyTri2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} oxyTri2.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} oxyTri2.downloadDir = oxyTri2 # defaults are OK: genbank and refseq mrna.native.load yes # genbank est.native.load yes refseq.mrna.xeno.load yes # genbank mrna and est xeno.load no # droAna1 (D. ananassae) droAna1.serverGenome = /hive/data/genomes/droAna1/droAna1.2bit droAna1.ooc = /hive/data/genomes/droAna1/11.ooc droAna1.lift = no droAna1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droAna1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droAna1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droAna1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droAna1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droAna1.refseq.mrna.native.load = no droAna1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse # GenBank has no D. ananassae ESTs at this point... that may change. droAna1.genbank.est.native.load = no droAna1.downloadDir = droAna1 droAna1.perChromTables = no # droAna2 (D. ananassae) droAna2.serverGenome = /hive/data/genomes/droAna2/droAna2.2bit droAna2.ooc = /hive/data/genomes/droAna2/11.ooc droAna2.lift = no droAna2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droAna2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droAna2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droAna2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droAna2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droAna2.refseq.mrna.native.load = no droAna2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse # GenBank has no D. ananassae ESTs at this point... that may change. droAna2.genbank.est.native.load = no droAna2.downloadDir = droAna2 droAna2.perChromTables = no # droMoj1 (D. mojavensis) droMoj1.serverGenome = /hive/data/genomes/droMoj1/droMoj1.2bit droMoj1.ooc = /hive/data/genomes/droMoj1/11.ooc droMoj1.lift = no droMoj1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droMoj1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droMoj1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droMoj1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droMoj1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droMoj1.refseq.mrna.native.load = no droMoj1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse # GenBank has no D. mojavensis ESTs at this point... that may change. droMoj1.genbank.est.native.load = no droMoj1.downloadDir = droMoj1 droMoj1.perChromTables = no # droMoj2 (D. mojavensis) # genbank has 1 mRNA and 0 ESTs at time of initial build droMoj2.serverGenome = /hive/data/genomes/droMoj2/droMoj2.2bit droMoj2.ooc = /hive/data/genomes/droMoj2/11.ooc droMoj2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droMoj2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droMoj2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droMoj2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droMoj2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droMoj2.lift = no droMoj2.refseq.mrna.native.load = no droMoj2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse droMoj2.genbank.est.native.load = no droMoj2.downloadDir = droMoj2 droMoj2.perChromTables = no # droVir1 (D. virilis) droVir1.serverGenome = /hive/data/genomes/droVir1/droVir1.2bit droVir1.ooc = /hive/data/genomes/droVir1/11.ooc droVir1.lift = no droVir1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droVir1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droVir1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droVir1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droVir1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droVir1.refseq.mrna.native.load = no droVir1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse # GenBank has no D. virilis ESTs at this point... that may change. droVir1.genbank.est.native.load = no droVir1.downloadDir = droVir1 droVir1.perChromTables = no # droVir2 (D. virilis) # genbank has 35 mRNAs and 633 ESTs at time of initial build droVir2.serverGenome = /hive/data/genomes/droVir2/droVir2.2bit droVir2.ooc = /hive/data/genomes/droVir2/11.ooc droVir2.lift = no droVir2.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droVir2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droVir2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droVir2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droVir2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droVir2.refseq.mrna.native.load = yes droVir2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse droVir2.genbank.est.native.load = yes droVir2.downloadDir = droVir2 droVir2.perChromTables = no # apiMel1 (A. mellifera) apiMel1.serverGenome = /hive/data/genomes/apiMel1/apiMel1.2bit apiMel1.ooc = /hive/data/genomes/apiMel2/11.ooc apiMel1.lift = no apiMel1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} apiMel1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} apiMel1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} apiMel1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} apiMel1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} apiMel1.refseq.mrna.native.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse apiMel1.downloadDir = apiMel1 apiMel1.perChromTables = no # apiMel2 (A. mellifera) apiMel2.serverGenome = /hive/data/genomes/apiMel2/nib/*.nib apiMel2.ooc = /hive/data/genomes/apiMel2/11.ooc apiMel2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} apiMel2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} apiMel2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} apiMel2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} apiMel2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} apiMel2.lift = no apiMel2.refseq.mrna.native.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse apiMel2.genbank.mrna.xeno.load = yes apiMel2.downloadDir = apiMel2 apiMel2.perChromTables = no # droEre1 (D. erecta) droEre1.serverGenome = /hive/data/genomes/droEre1/droEre1.2bit droEre1.ooc = /hive/data/genomes/droEre1/11.ooc droEre1.lift = no droEre1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droEre1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droEre1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droEre1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droEre1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droEre1.refseq.mrna.native.load = no droEre1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse droEre1.genbank.mrna.xeno.load = yes # GenBank has no D. erecta ESTs at this point... that may change. droEre1.genbank.est.native.load = no droEre1.downloadDir = droEre1 droEre1.perChromTables = no # monDom5 (M. domestica) 8 chroms plus X and Un monDom5.serverGenome = /hive/data/genomes/monDom5/monDom5.2bit monDom5.ooc = /hive/data/genomes/monDom5/11.ooc monDom5.lift = /hive/data/genomes/monDom5/jkStuff/liftAll.lft monDom5.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} monDom5.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} monDom5.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} monDom5.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} monDom5.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} monDom5.downloadDir = monDom5 monDom5.refseq.mrna.xeno.load = yes monDom5.refseq.mrna.xeno.loadDesc = yes monDom5.genbank.mrna.xeno.load = yes monDom5.perChromTables = no monDom5.upstreamGeneTbl = refGene monDom5.upstreamMaf = multiz9way /hive/data/genomes/monDom5/bed/multiz9way/species.lst # monDom4 (M. domestica) 8 chroms plus X and Un monDom4.serverGenome = /hive/data/genomes/monDom4/monDom4.2bit monDom4.ooc = /hive/data/genomes/monDom4/11.ooc monDom4.lift = no monDom4.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} monDom4.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} monDom4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} monDom4.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} monDom4.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} monDom4.downloadDir = monDom4 monDom4.refseq.mrna.xeno.load = yes monDom4.refseq.mrna.xeno.loadDesc = yes monDom4.upstreamGeneTbl = ensGene monDom4.upstreamMaf = multiz7way /hive/data/genomes/monDom4/bed/multiz7way/species.lst # monDom1 (M. domestica) 19,348 scaffolds monDom1.serverGenome = /hive/data/genomes/monDom1/monDom1.2bit monDom1.ooc = /hive/data/genomes/monDom1/11.ooc monDom1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} monDom1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} monDom1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} monDom1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} monDom1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} monDom1.refseq.mrna.native.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse monDom1.genbank.est.native.load = no monDom1.downloadDir = monDom1 monDom1.lift = no monDom1.perChromTables = no # there is no suitable gene table here # monDom1.upstreamGeneTbl = ensGene # cb3 (C. briggsae) cb3.serverGenome = /hive/data/genomes/cb3/cb3.2bit cb3.ooc = /hive/data/genomes/cb3/11.ooc cb3.lift = /hive/data/genomes/cb3/jkStuff/liftAll.lft cb3.align.unplacedChroms = chrUn,chr*_random cb3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} cb3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} cb3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} cb3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} cb3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} cb3.refseq.mrna.native.load = no cb3.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse cb3.genbank.mrna.xeno.load = yes cb3.downloadDir = cb3 # cb1 (C. briggsae) cb1.serverGenome = /hive/data/genomes/cb1/chrUn.2bit cb1.ooc = /hive/data/genomes/cb1/11.ooc cb1.align.unplacedChroms = chrUn cb1.lift = /hive/data/genomes/cb1/Un/chrUn.lft cb1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} cb1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} cb1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} cb1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} cb1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} cb1.refseq.mrna.native.load = yes cb1.refseq.mrna.xeno.load = yes cb1.genbank.mrna.xeno.load = no cb1.downloadDir = cbJul2002 cb1.perChromTables = no # droSim1 (D. simulans) droSim1.serverGenome = /hive/data/genomes/droSim1/droSim1.2bit droSim1.ooc = /hive/data/genomes/droSim1/11.ooc droSim1.lift = /hive/data/genomes/droSim1/jkStuff/liftAll.lft droSim1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droSim1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droSim1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droSim1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droSim1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droSim1.refseq.mrna.native.load = no droSim1.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse droSim1.genbank.mrna.xeno.load = yes droSim1.downloadDir = droSim1 # droGri1 (D. grimshawi) droGri1.serverGenome = /hive/data/genomes/droGri1/droGri1.2bit droGri1.lift = no droGri1.ooc=/hive/data/genomes/droGri1/11.ooc droGri1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droGri1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droGri1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droGri1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droGri1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droGri1.refseq.mrna.native.load = no droGri1.refseq.mrna.xeno.load = yes # GenBank has no D. grimshawi mRNAs nor ESTs at this point... that may change. droGri1.genbank.mrna.native.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse droGri1.genbank.est.native.load = no droGri1.downloadDir = droGri1 droGri1.perChromTables = no # droYak2 (D. yakuba) droYak2.serverGenome = /hive/data/genomes/droYak2/droYak2.2bit droYak2.ooc = /hive/data/genomes/droYak2/11.ooc droYak2.lift = /hive/data/genomes/droYak2/jkStuff/liftAll.lft droYak2.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} droYak2.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} droYak2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} droYak2.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} droYak2.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} droYak2.refseq.mrna.native.load = no droYak2.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse droYak2.downloadDir = droYak2 # droPer1 (D. persimilis) # genbank.150.0/full has 1 mRNA and 0 ESTs at time of initial build, # so no need to make native tracks. droPer1.serverGenome = /hive/data/genomes/droPer1/droPer1.2bit droPer1.ooc = /hive/data/genomes/droPer1/11.ooc droPer1.lift = no droPer1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droPer1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droPer1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droPer1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droPer1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droPer1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} droPer1.refseq.mrna.native.load = no droPer1.refseq.mrna.xeno.load = yes droPer1.genbank.mrna.native.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse droPer1.genbank.est.native.load = no droPer1.downloadDir = droPer1 droPer1.perChromTables = no # droSec1 (D. sechellia) # genbank.150.0/full has 7 mRNAs and 0 ESTs at time of initial build, # so no need to make native tracks. droSec1.serverGenome = /hive/data/genomes/droSec1/droSec1.2bit droSec1.ooc = /hive/data/genomes/droSec1/11.ooc droSec1.lift = no droSec1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} droSec1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} droSec1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} droSec1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} droSec1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} droSec1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} droSec1.refseq.mrna.native.load = no droSec1.refseq.mrna.xeno.load = yes droSec1.genbank.mrna.native.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse droSec1.genbank.mrna.xeno.load = yes droSec1.genbank.est.native.load = no droSec1.downloadDir = droSec1 droSec1.perChromTables = no # nemVec1 (Starlet Sea Anemone) # Per Mark: only load if >10^3 available - /hive/data/genomes/genbank/data/organism.lst # organism mrnaCnt estCnt refSeqCnt nemVec1.serverGenome = /hive/data/genomes/nemVec1/nemVec1.2bit nemVec1.ooc = /hive/data/genomes/nemVec1/11.ooc nemVec1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} nemVec1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} nemVec1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} nemVec1.maxIntron = 100000 nemVec1.lift = no nemVec1.genbank.est.native.load = yes nemVec1.genbank.est.xeno.load = no nemVec1.genbank.mrna.native.load = no # DO NOT NEED genbank.mrna.xeno except for human, mouse nemVec1.refseq.mrna.xeno.load = yes nemVec1.refseq.mrna.native.load = no nemVec1.perChromTables = no nemVec1.downloadDir = nemVec1 # aplCal1 - (Sea Hare Broad WGS Aplcal 2.0) # Assembly Accession: AASC00000000.2 aplCal1.serverGenome = /hive/data/genomes/aplCal1/aplCal1.2bit aplCal1.ooc = /hive/data/genomes/aplCal1/11.ooc aplCal1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} aplCal1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} aplCal1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} aplCal1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} aplCal1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} aplCal1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} aplCal1.refseq.mrna.native.load = no aplCal1.genbank.est.native.load = yes aplCal1.genbank.est.xeno.load = no aplCal1.refseq.mrna.xeno.load = yes aplCal1.refseq.mrna.xeno.loadDesc = yes aplCal1.perChromTables = no aplCal1.downloadDir = aplCal1 aplCal1.genbank.mrna.blatTargetDb = yes aplCal1.lift = no # staAur2 (Staphylococcus aureus - Taxid: 93061) staAur2.serverGenome = /hive/data/genomes/staAur2/staAur2.2bit staAur2.ooc = /hive/data/genomes/staAur2/jkStuff/staAur2.11.ooc staAur2.lift = no staAur2.downloadDir = staAur2 staAur2.perChromTables = no staAur2.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} staAur2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} staAur2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} staAur2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} staAur2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc # staAur2.upstreamGeneTbl = ensGene # staAur2.upstreamMaf = multiz9way /hive/data/genomes/staAur2/bed/multiz9way/species.list # staAur1 (Staphylococcus aureus - Taxid: 93061) staAur1.serverGenome = /hive/data/genomes/staAur1/staAur1.2bit staAur1.ooc = /hive/data/genomes/staAur1/jkStuff/staAur1.11.ooc staAur1.lift = no staAur1.downloadDir = staAur1 staAur1.perChromTables = no staAur1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} staAur1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} staAur1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} staAur1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} staAur1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc # staAur1.upstreamGeneTbl = ensGene # staAur1.upstreamMaf = multiz9way /hive/data/genomes/staAur1/bed/multiz9way/species.list # hbv1 (Hepatitis B virus - Taxid: 10407) hbv1.serverGenome = /hive/data/genomes/hbv1/hbv1.2bit hbv1.ooc = /hive/data/genomes/hbv1/jkStuff/hbv1.11.ooc hbv1.lift = no hbv1.downloadDir = hbv1 hbv1.perChromTables = no hbv1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} hbv1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} hbv1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} hbv1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} hbv1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # trying mrna.xeno to see what loads hbv1.genbank.mrna.xeno.load = yes hbv1.genbank.mrna.xeno.loadDesc = yes hbv1.refseq.mrna.xeno.load = yes hbv1.refseq.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc # hbv1.upstreamGeneTbl = ensGene # hbv1.upstreamMaf = multiz9way /hive/data/genomes/hbv1/bed/multiz9way/species.list # hpv1 (Human papillomavirus type 90 - Taxid: 333769) hpv1.serverGenome = /hive/data/genomes/hpv1/hpv1.2bit hpv1.ooc = /hive/data/genomes/hpv1/jkStuff/hpv1.11.ooc hpv1.lift = no hpv1.downloadDir = hpv1 hpv1.perChromTables = no hpv1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} hpv1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} hpv1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} hpv1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} hpv1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc # hpv1.upstreamGeneTbl = ensGene # hpv1.upstreamMaf = multiz9way /hive/data/genomes/hpv1/bed/multiz9way/species.list # wuhCor1 (Severse acute respiratory syndrome coronavirus 2 - Taxid: 2697049) wuhCor1.serverGenome = /hive/data/genomes/wuhCor1/wuhCor1.2bit wuhCor1.ooc = /hive/data/genomes/wuhCor1/jkStuff/wuhCor1.11.ooc wuhCor1.lift = no wuhCor1.downloadDir = wuhCor1 wuhCor1.perChromTables = no wuhCor1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} wuhCor1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} wuhCor1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} wuhCor1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} wuhCor1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # # Please keep organisms together and in assending order rather than adding at # the end #